Mercurial > repos > iuc > jbrowse
annotate jbrowse.xml @ 6:ecbdfc775b9a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 16:44:39 -0400 |
| parents | ae9382cfb6ac |
| children | ad4b9d7eae6a |
| rev | line source |
|---|---|
|
6
ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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1 <tool id="jbrowse" name="JBrowse" version="0.5.2"> |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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changeset
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2 <description>genome browser</description> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
changeset
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3 <macros> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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changeset
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4 <import>macros.xml</import> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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5 </macros> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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changeset
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6 <expand macro="requirements"/> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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changeset
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7 <expand macro="stdio"/> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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8 <version_command>python jbrowse.py --version</version_command> |
| 3 | 9 <command><![CDATA[ |
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5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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10 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
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11 #if $action.action_select == "create": |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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changeset
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12 mkdir -p $output.files_path; |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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13 #else: |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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14 cp -R $action.update_jbrowse.extra_files_path $output.files_path; |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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15 #end if |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
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16 |
| 3 | 17 ## Copy the XML file into the directory, mostly for debugging |
| 18 ## but nice if users want to reproduce locally | |
| 19 cp $trackxml $output.files_path/galaxy.xml && | |
| 20 | |
| 21 ## Once that's done, we run the python script to handle the real work | |
| 22 python $__tool_directory__/jbrowse.py | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
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23 |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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changeset
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24 --jbrowse \${JBROWSE_SOURCE_DIR} |
| 3 | 25 #if str($standalone) == "Complete": |
| 26 --standalone | |
| 27 #end if | |
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5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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28 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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29 --outdir $output.files_path |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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30 $trackxml; |
| 3 | 31 |
| 32 #if str($standalone) == "Complete": | |
| 33 mv $output.files_path/index.html $output; | |
| 34 #else: | |
| 35 mv $dummyIndex $output; | |
| 36 #end if | |
| 37 | |
| 38 | |
| 39 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. | |
| 40 #if str($uglyTestingHack) == "enabled": | |
| 41 mv $trackxml $output | |
| 42 #end if | |
| 43 ]]></command> | |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
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changeset
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44 <configfiles> |
| 3 | 45 <configfile name="dummyIndex"> |
| 46 <![CDATA[ | |
| 47 <html> | |
| 48 <head> | |
| 49 </head> | |
| 50 <body> | |
| 51 <h1>JBrowse Data Directory</h1> | |
| 52 <p> | |
| 53 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?) | |
| 54 started shipping with the ability to produce just the | |
| 55 "data" directory from a JBrowse instance, rather than a | |
| 56 complete, standalone instance. This was intended to be used | |
| 57 with the in-development Apollo integration, but may have other | |
| 58 uses as well. | |
| 59 </p> | |
| 60 <p> | |
| 61 <u>This is not usable on its own</u>. The output dataset may be | |
| 62 used with Apollo, or may be passed through the "JBrowse - | |
| 63 Convert to Standalone" tool in Galaxy to "upgrade" to a full | |
| 64 JBrowse instance. | |
| 65 </p> | |
| 66 </body> | |
| 67 </html> | |
| 68 ]]> | |
| 69 </configfile> | |
| 70 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> | |
| 71 <root> | |
| 72 <metadata> | |
| 73 <gencode>$gencode</gencode> | |
| 74 <genomes> | |
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6
ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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75 #if str($action.reference_genome.genome_type_select) == "indexed": |
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ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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76 <genome>${action.reference_genome.genomes.fields.path}</genome> |
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ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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77 #else |
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ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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78 #for $genome in $action.reference_genome.genomes: |
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ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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79 <genome>$genome</genome> |
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ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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80 #end for |
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ecbdfc775b9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
iuc
parents:
5
diff
changeset
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81 #end if |
| 3 | 82 </genomes> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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83 <general> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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84 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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85 <trackPadding>${jbgen.trackPadding}</trackPadding> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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86 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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87 <shareLink>${jbgen.shareLink}</shareLink> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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88 <aboutDescription>${jbgen.aboutDescription}</aboutDescription> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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89 <show_tracklist>${jbgen.show_tracklist}</show_tracklist> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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90 <show_nav>${jbgen.show_nav}</show_nav> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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91 <show_overview>${jbgen.show_overview}</show_overview> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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92 <show_menu>${jbgen.show_menu}</show_menu> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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93 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
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94 </general> |
| 3 | 95 </metadata> |
| 96 <tracks> | |
| 97 #for $tg in $track_groups: | |
| 98 #for $track in $tg.data_tracks: | |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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99 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
| 3 | 100 <files> |
| 101 #for $dataset in $track.data_format.annotation: | |
| 102 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" /> | |
| 103 #end for | |
| 104 </files> | |
| 105 | |
| 106 <options> | |
| 107 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast": | |
| 108 <style> | |
| 109 <className>${track.data_format.jbstyle.style_classname}</className> | |
| 110 <description>${track.data_format.jbstyle.style_description}</description> | |
| 111 <label>${track.data_format.jbstyle.style_label}</label> | |
| 112 <height>${track.data_format.jbstyle.style_height}</height> | |
| 113 </style> | |
| 114 <scaling> | |
| 115 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none": | |
| 116 <method>ignore</method> | |
| 117 <scheme> | |
| 118 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic": | |
| 119 <color>__auto__</color> | |
| 120 #else | |
| 121 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color> | |
| 122 #end if | |
| 123 </scheme> | |
| 124 #else | |
| 125 <method>score</method> | |
| 126 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo> | |
| 127 <scales> | |
| 128 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type> | |
| 129 | |
| 130 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual": | |
| 131 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min> | |
| 132 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max> | |
| 133 #end if | |
| 134 </scales> | |
| 135 <scheme> | |
| 136 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type> | |
| 137 ## auto_color | |
| 138 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity": | |
| 139 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic": | |
| 140 <color>__auto__</color> | |
| 141 #else | |
| 142 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color> | |
| 143 #end if | |
| 144 #end if | |
| 145 </scheme> | |
| 146 #end if | |
| 147 </scaling> | |
| 148 #end if | |
| 149 | |
| 150 #if str($track.data_format.data_format_select) == "wiggle": | |
| 151 <wiggle> | |
| 152 <type>${track.data_format.xyplot}</type> | |
| 153 <variance_band>${track.data_format.var_band}</variance_band> | |
| 154 #if str($track.data_format.scaling.scale_select) == "auto_local": | |
| 155 <autoscale>local</autoscale> | |
| 156 #else if str($track.data_format.scaling.scale_select) == "auto_global": | |
| 157 <autoscale>global</autoscale> | |
| 158 #else: | |
| 159 <min>${track.data_format.scaling.minimum}</min> | |
| 160 <max>${track.data_format.scaling.maximum}</max> | |
| 161 #end if | |
| 162 | |
| 163 ## Wiggle tracks need special color config | |
| 164 #if str($track.data_format.jbcolor.color.color_select) != "automatic": | |
| 165 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos> | |
| 166 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg> | |
| 167 #else: | |
| 168 <color_pos>__auto__</color_pos> | |
| 169 <color_neg>__auto__</color_neg> | |
| 170 #end if | |
| 171 | |
| 172 ## Bicolor pivot config | |
| 173 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero": | |
| 174 <bicolor_pivot>zero</bicolor_pivot> | |
| 175 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean": | |
| 176 <bicolor_pivot>mean</bicolor_pivot> | |
| 177 #else: | |
| 178 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot> | |
| 179 #end if | |
| 180 </wiggle> | |
| 181 #else if str($track.data_format.data_format_select) == "pileup": | |
| 182 <pileup> | |
| 183 <auto_snp>${track.data_format.auto_snp}</auto_snp> | |
| 184 <bam_indices> | |
| 185 #for $dataset in $track.data_format.annotation: | |
| 186 <bam_index>${dataset.metadata.bam_index}</bam_index> | |
| 187 #end for | |
| 188 </bam_indices> | |
| 189 </pileup> | |
| 190 #else if str($track.data_format.data_format_select) == "blast": | |
| 191 <blast> | |
| 192 #if str($track.data_format.blast_parent) != "": | |
| 193 <parent>${track.data_format.blast_parent}</parent> | |
| 194 #end if | |
| 195 <protein>${track.data_format.is_protein}</protein> | |
| 196 <min_gap>${track.data_format.min_gap}</min_gap> | |
| 197 </blast> | |
| 198 #else if str($track.data_format.data_format_select) == "gene_calls": | |
| 199 <gff> | |
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5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
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200 <trackType>${track.data_format.track_class}</trackType> |
| 3 | 201 #if $track.data_format.match_part.match_part_select: |
| 202 <match>${track.data_format.match_part.name}</match> | |
| 203 #end if | |
| 204 </gff> | |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
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205 ## #else if str($track.data_format.data_format_select) == "sparql": |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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206 ## <sparql> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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207 ## <url>${track.data_format.url}</url> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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208 ## <label>${track.data_format.label}</label> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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209 ## <!-- This is going to be an absolutey nightmare --> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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210 ## <query>${track.data_format.query}</query> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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211 ## </sparql> |
| 3 | 212 #end if |
| 213 </options> | |
| 214 </track> | |
| 215 #end for | |
| 216 #end for | |
| 217 </tracks> | |
| 218 </root> | |
| 219 ]]> | |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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220 </configfile> |
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221 </configfiles> |
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222 <inputs> |
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223 <conditional name="action" label="Action"> |
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224 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> |
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225 <option value="create">New JBrowse Instance</option> |
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226 <option value="update">Update exising JBrowse Instance</option> |
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227 </param> |
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228 <when value="create"> |
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229 <expand macro="genome_selector" /> |
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230 </when> |
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231 <when value="update"> |
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232 <expand macro="genome_selector" |
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233 label="Additional Fasta Sequence(s)" |
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234 help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences." |
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235 optional="True"/> |
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236 <param label="Previous JBrowse Instance" |
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237 name="update_jbrowse" |
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238 type="data" |
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239 format="html" /> |
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240 </when> |
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241 </conditional> |
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242 |
| 3 | 243 <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/> |
| 244 | |
| 245 <param label="Genetic Code" name="gencode" type="select"> | |
| 246 <option value="1">1. The Standard Code</option> | |
| 247 <option value="2">2. The Vertebrate Mitochondrial Code</option> | |
| 248 <option value="3">3. The Yeast Mitochondrial Code</option> | |
| 249 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
| 250 <option value="5">5. The Invertebrate Mitochondrial Code</option> | |
| 251 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
| 252 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option> | |
| 253 <option value="10">10. The Euplotid Nuclear Code</option> | |
| 254 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option> | |
| 255 <option value="12">12. The Alternative Yeast Nuclear Code</option> | |
| 256 <option value="13">13. The Ascidian Mitochondrial Code</option> | |
| 257 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option> | |
| 258 <option value="16">16. Chlorophycean Mitochondrial Code</option> | |
| 259 <option value="21">21. Trematode Mitochondrial Code</option> | |
| 260 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option> | |
| 261 <option value="23">23. Thraustochytrium Mitochondrial Code</option> | |
| 262 <option value="24">24. Pterobranchia Mitochondrial Code</option> | |
| 263 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> | |
| 264 </param> | |
| 265 | |
| 266 <repeat name="track_groups" title="Track Group"> | |
| 267 <param label="Track Category" | |
| 268 name="category" | |
| 269 type="text" | |
| 270 value="Default" | |
| 271 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/> | |
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272 <repeat name="data_tracks" title="Annotation Track"> |
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273 <conditional name="data_format" label="Track Options"> |
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274 <param type="select" label="Track Type" name="data_format_select"> |
| 3 | 275 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> |
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276 <option value="pileup">BAM Pileups</option> |
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277 <option value="blast">Blast XML</option> |
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278 <option value="wiggle">BigWig XY</option> |
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279 <option value="vcf">VCF SNPs</option> |
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280 <!--<option value="sparql">SPARQL</option>--> |
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281 </param> |
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282 <when value="blast"> |
| 3 | 283 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> |
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284 |
| 3 | 285 <param label="Features used in Blast Search" |
| 286 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this." | |
| 287 format="gff3" | |
| 288 name="blast_parent" | |
| 289 optional="true" | |
| 290 type="data"/> | |
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291 |
| 3 | 292 <param label="Minimum Gap Size" |
| 293 help="before a new match_part feature is created" | |
| 294 name="min_gap" | |
| 295 type="integer" | |
| 296 value="10" | |
| 297 min="2" /> | |
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298 <param label="Is this a protein blast search?" |
| 3 | 299 type="boolean" |
| 300 name="is_protein" | |
| 301 truevalue="true" | |
| 302 falsevalue="false" /> | |
| 303 | |
| 304 <expand macro="track_styling" | |
| 305 classname="feature" | |
| 306 label="description" | |
| 307 description="Hit_titles" | |
| 308 height="600px"/> | |
| 309 <expand macro="color_selection" | |
| 310 token_scaling_lin_select="false" | |
| 311 token_scaling_log_select="true" /> | |
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312 <expand macro="track_display" /> |
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313 </when> |
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314 <when value="vcf"> |
| 3 | 315 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> |
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316 <expand macro="track_display" /> |
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317 </when> |
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318 <when value="gene_calls"> |
| 3 | 319 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> |
| 320 <conditional name="match_part" label="match/match_part data"> | |
| 321 <param label="This is match/match_part data" | |
| 322 type="boolean" | |
| 323 name="match_part_select" | |
| 324 truevalue="true" | |
| 325 falsevalue="false" /> | |
| 326 <when value="true"> | |
| 327 <param label="Match Part Feature Type" | |
| 328 name="name" | |
| 329 type="text" | |
| 330 value="match" | |
| 331 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here" | |
| 332 optional="False"/> | |
| 333 </when> | |
| 334 <when value="false" /> | |
| 335 </conditional> | |
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336 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> |
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337 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> |
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338 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> |
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339 </param> |
| 3 | 340 <expand macro="track_styling" /> |
| 341 <expand macro="color_selection" /> | |
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342 <expand macro="track_display" /> |
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343 </when> |
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344 <when value="pileup"> |
| 3 | 345 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
| 346 <param label="Autogenerate SNP Track" | |
| 347 help="Not recommended for deep coverage BAM files" | |
| 348 type="boolean" | |
| 349 name="auto_snp" | |
| 350 truevalue="true" | |
| 351 falsevalue="false" /> | |
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352 <expand macro="track_display" /> |
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353 </when> |
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354 <when value="wiggle"> |
| 3 | 355 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
| 356 | |
| 357 <param label="Use XYPlot" | |
| 358 help="instead of continuous colored band" | |
| 359 type="boolean" | |
| 360 name="xyplot" | |
| 361 truevalue="JBrowse/View/Track/Wiggle/XYPlot" | |
| 362 falsevalue="JBrowse/View/Track/Wiggle/Density" /> | |
| 363 <param label="Show variance band" | |
| 364 help="Only for XYPlots" | |
| 365 type="boolean" | |
| 366 name="var_band" | |
| 367 truevalue="true" | |
| 368 falsevalue="false" /> | |
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369 |
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370 <conditional name="scaling" label="Scaling"> |
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371 <param type="select" label="Track Scaling" name="scale_select"> |
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372 <option value="auto_local">Autoscale (local)</option> |
| 3 | 373 <option value="auto_global" selected="true">Autoscale (global)</option> |
| 374 <option value="fixed">Specify Min/Max</option> | |
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375 </param> |
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376 <when value="auto_local"></when> |
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377 <when value="auto_global"></when> |
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378 <when value="fixed"> |
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379 <param label="Track minimum" name="minimum" |
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380 type="integer" value="0" /> |
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381 <param label="Track maximum" name="maximum" |
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382 type="integer" value="100" /> |
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383 </when> |
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384 </conditional> |
| 3 | 385 <expand macro="color_selection_minmax" /> |
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386 <expand macro="track_display" /> |
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387 </when> |
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388 <!-- |
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389 <when value="sparql"> |
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390 <param type="text" label="SPARQL Server URL" name="url" /> |
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391 <param type="text" label="Track Label" name="key" value="SPARQL Genes" /> |
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392 <param type="text" label="SPARQL Query" name="query" area="true" /> |
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393 <expand macro="track_display" /> |
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394 </when> |
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395 --> |
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396 </conditional> |
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397 </repeat> |
| 3 | 398 </repeat> |
| 399 | |
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400 <expand macro="general_options" /> |
| 3 | 401 <param type="hidden" name="uglyTestingHack" value="" /> |
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402 </inputs> |
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403 <outputs> |
| 3 | 404 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/> |
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405 </outputs> |
| 3 | 406 <tests> |
| 407 <test> | |
| 408 <!-- gencode --> | |
| 409 <param name="genomes" value="merlin.fa"/> | |
| 410 <param name="gencode" value="1" /> | |
| 411 <param name="standalone" value="Data Directory" /> | |
| 412 <param name="uglyTestingHack" value="enabled" /> | |
| 413 <output name="output" file="gencode/test-1.xml" lines_diff="4" /> | |
| 414 </test> | |
| 415 <test> | |
| 416 <param name="genomes" value="merlin.fa"/> | |
| 417 <param name="gencode" value="11" /> | |
| 418 <param name="standalone" value="Data Directory" /> | |
| 419 <param name="uglyTestingHack" value="enabled" /> | |
| 420 <output name="output" file="gencode/test.xml" lines_diff="4"/> | |
| 421 </test> | |
| 422 <!-- | |
| 423 <test> | |
| 424 <param name="genomes" value="merlin.fa"/> | |
| 425 <param name="gencode" value="11" /> | |
| 426 <param name="standalone" value="Data Directory" /> | |
| 427 <param name="track_groups_0|category" value="Auto Coloured" /> | |
| 428 <param name="track_groups_0|data_tracks_0|data_format" value="gene_calls"/> | |
| 429 <param name="track_groups_0|data_tracks_0|annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> | |
| 430 <param name="track_groups_0|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 431 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 432 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> | |
| 433 | |
| 434 | |
| 435 <param name="track_groups_1|category" value="Ignore Scale" /> | |
| 436 <param name="track_groups_1|data_tracks_0|data_format" value="gene_calls"/> | |
| 437 <param name="track_groups_1|data_tracks_0|annotation" value="gff3/1.gff"/> | |
| 438 <param name="track_groups_1|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 439 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 440 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|color_select" value="manual"/> | |
| 441 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|style_color" value="#ff00ff"/> | |
| 442 | |
| 443 <param name="track_groups_2|category" value="Scaled Colour" /> | |
| 444 <param name="track_groups_2|data_tracks_0|data_format" value="gene_calls"/> | |
| 445 <param name="track_groups_2|data_tracks_0|annotation" value="gff3/1.gff"/> | |
| 446 <param name="track_groups_2|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 447 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 448 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 449 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 450 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 451 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> | |
| 452 <param name="track_groups_2|data_tracks_1|data_format" value="gene_calls"/> | |
| 453 <param name="track_groups_2|data_tracks_1|annotation" value="gff3/1.gff"/> | |
| 454 <param name="track_groups_2|data_tracks_1|match_part|match_part_select" value="false"/> | |
| 455 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 456 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 457 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 458 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 459 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> | |
| 460 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|style_color" value="#0000ff"/> | |
| 461 <param name="track_groups_2|data_tracks_2|data_format" value="gene_calls"/> | |
| 462 <param name="track_groups_2|data_tracks_2|annotation" value="gff3/1.gff"/> | |
| 463 <param name="track_groups_2|data_tracks_2|match_part|match_part_select" value="false"/> | |
| 464 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 465 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 466 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 467 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|minimum" value="0"/> | |
| 468 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> | |
| 469 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 470 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> | |
| 471 <param name="track_groups_2|data_tracks_3|data_format" value="gene_calls"/> | |
| 472 <param name="track_groups_2|data_tracks_3|annotation" value="gff3/1.gff"/> | |
| 473 <param name="track_groups_2|data_tracks_3|match_part|match_part_select" value="false"/> | |
| 474 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 475 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 476 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 477 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|minimum" value="0"/> | |
| 478 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> | |
| 479 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 480 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> | |
| 481 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|style_color" value="#ff0000"/> | |
| 482 | |
| 483 <param name="track_groups_3|category" value="Realistic" /> | |
| 484 <param name="track_groups_3|data_tracks_0|data_format" value="gene_calls"/> | |
| 485 <param name="track_groups_3|data_tracks_0|annotation" value="gff3/interpro.gff"/> | |
| 486 <param name="track_groups_3|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 487 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 488 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> | |
| 489 <param name="track_groups_3|data_tracks_1|data_format" value="gene_calls"/> | |
| 490 <param name="track_groups_3|data_tracks_1|annotation" value="gff3/2.gff"/> | |
| 491 <param name="track_groups_3|data_tracks_1|match_part|match_part_select" value="true"/> | |
| 492 <param name="track_groups_3|data_tracks_1|match_part|name" value="cDNA_match"/> | |
| 493 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 494 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color|color_select" value="automatic"/> | |
| 495 | |
| 496 <param name="uglyTestingHack" value="enabled" /> | |
| 497 <output name="output" file="gff3/test.xml" /> | |
| 498 </test> | |
| 499 --> | |
| 500 </tests> | |
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501 <help><![CDATA[ |
| 3 | 502 JBrowse-in-Galaxy |
| 503 ================= | |
| 504 | |
| 505 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible | |
| 506 alternative to Trackster. | |
| 507 | |
|
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508 Overview |
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509 -------- |
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510 |
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511 JBrowse is a fast, embeddable genome browser built completely with |
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512 JavaScript and HTML5. |
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513 |
| 3 | 514 The JBrowse-in-Galaxy (JiG) tool was written to help build complex |
| 515 JBrowse installations straight from Galaxy, taking advantage of the | |
| 516 latest Galaxy features such as dataset collections, sections, and colour | |
| 517 pickers. It allows you to build up a JBrowse instance without worrying | |
| 518 about how to run the command line tools to format your data, and which | |
| 519 options need to be supplied and where. Additionally it comes with many | |
| 520 javascript functions to handle colouring of features which would be | |
| 521 nearly impossible to write without the assistance of this tool. | |
| 522 | |
| 523 The JBrowse-in-Galaxy tool is maintained by `Eric | |
| 524 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you | |
| 525 encounter missing features or bugs. | |
| 526 | |
| 527 Options | |
| 528 ------- | |
| 529 | |
| 530 The first option you encounter is the **Fasta Sequence(s)**. This option | |
| 531 now accepts multiple fasta files, allowing you to build JBrowse | |
| 532 instances that contain data for multiple genomes or chrosomomes | |
| 533 (generally known as "landmark features" in gff3 terminology.) Up to 30 | |
| 534 will be shown from the dropdown selector within JBrowse, this is a known | |
| 535 issue. | |
| 536 | |
| 537 **Standalone Instances** are a somewhat in-development feature. | |
| 538 Currently Galaxy copies the entire JBrowse directory in order to have a | |
| 539 complete, downloadable file that contains a ready-to-go JBrowse | |
| 540 instance. This is obviously an anti-feature because users don't want a | |
| 541 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse | |
| 542 dataset in their history, and admins don't want useless copies of | |
| 543 JBrowse on disk. Unfortunately we have not come up with the perfect | |
| 544 solution just yet, but we're working on it! In the meantime, users have | |
| 545 been given the option to produce just the ``data/`` directory. For those | |
| 546 unfamiliar with JBrowse, the ``data/`` directory contains processed data | |
| 547 files, but no way to view them. This feature is additionally implemented | |
| 548 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration. | |
| 549 | |
| 550 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse, | |
| 551 which allows users to specify a non standard genetic code, and have | |
| 552 JBrowse highlight the correct start and stop codons. If you would like | |
| 553 to use a coding table not provided by this list, please let | |
| 554 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for | |
| 555 this. | |
| 556 | |
| 557 **Track Groups** represent a set of tracks in a single category. These | |
| 558 can be used to let your users understand relationships between large | |
| 559 groups of tracks. | |
| 560 | |
| 561 .. image:: sections.png | |
| 562 | |
| 563 Annotation Tracks | |
| 564 ----------------- | |
| 565 | |
| 566 Within Track Groups, you have one or more **Annotation Tracks**. Each | |
| 567 Annotation Track is a groups of datasets which have similar styling. | |
| 568 This allows you to rapidly build up JBrowse instances without having to | |
| 569 configure tracks individually. A massive improvement over previous | |
| 570 versions. For example, if you have five different GFF3 files from | |
| 571 various gene callers that you wish to display, you can take advantage of | |
| 572 this feature to style all of them similarly. | |
| 573 | |
| 574 There are a few different types of tracks supported, each with their own | |
| 575 set of options: | |
| 576 | |
| 577 GFF3/BED/GBK | |
| 578 ~~~~~~~~~~~~ | |
| 579 | |
| 580 These are your standard feature tracks. They usually highlight genes, | |
| 581 mRNAs and other features of interest along a genomic region. The | |
| 582 underlying tool and this help documentation focus primarily on GFF3 | |
| 583 data, and have not been tested extensively with other formats. Automatic | |
| 584 min/max detection will likely fail under BED and GBK datasets. | |
| 585 | |
| 586 The data may be of a subclass we call **match/match part** data. This | |
| 587 consists of top level ``match`` features, with a child ``match_part`` | |
| 588 feature, and is often used in displaying alignments. (See "Alignments" | |
| 589 section on the `GFF3 | |
| 590 specification <http://www.sequenceontology.org/gff3.shtml>`__ for more | |
| 591 information). If the data is match/match part, you will need to specify | |
| 592 the top level match feature name, as it can be one of a few different SO | |
| 593 terms, and JiG does not yet have the ability to understand SO terms. | |
| 594 | |
| 595 Next up is the **Styling Options** section, which lets you control a few | |
| 596 properties on how the track is styled. Most of these you will not need | |
| 597 to configure and can safely leave on defaults. Occasionally you will | |
| 598 want to change what information is shown in the end product. | |
| 599 | |
| 600 .. image:: styling.png | |
| 601 | |
| 602 In the above image you can see some black text, and some blue text. The | |
| 603 source of the black text is configured with the **style.label** option, | |
| 604 and the source of the blue text is configured with the | |
| 605 **style.description** option. | |
| 606 | |
| 607 Feature Score Scaling & Colouring Options | |
| 608 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 609 | |
| 610 First, you need to choose between ignoring the score attribute of GFF3 | |
| 611 files, or using it. If you choose to ignore it, all features will be | |
| 612 coloured with a solid colour. If you choose to use it, features will | |
| 613 have slightly different colours based on their scores. | |
| 614 | |
| 615 .. image:: opacity.png | |
| 616 | |
| 617 If you choose **Ignore score**, you may choose between automatically | |
| 618 choosing a colour, or manually specifying one. The automatically chosen | |
| 619 colours vary along a brewer palette and generally look quite nice with | |
| 620 no human intervention required. The manual colour choice is somewhat | |
| 621 self explanatory. Clicking on the small coloured square will bring up a | |
| 622 colour palette. | |
| 623 | |
| 624 If you choose **Base on score**, you're faced with a dizzying array of | |
| 625 options. First is the function to map the colour choices to colour | |
| 626 values. JiG comes with a few functions built in such as linear scaling, | |
| 627 logarithmic scaling, and blast scaling. | |
| 628 | |
| 629 The **linear scaling** method says "take these values, and they map | |
| 630 directly to a range of output values". **Logarithmic scaling** says | |
| 631 "please take the log of the score before mapping", and **Blast scaling** | |
| 632 is further specialised to handle blast data more nicely. These are | |
| 633 convenience functions to help transform the wide array of possible | |
| 634 values in the GFF3 score attribute to more meaningful numbers. If you | |
| 635 need more comprehensive score scaling, it is recommended that you | |
| 636 pre-process your GFF3 files somehow. | |
| 637 | |
| 638 Once you've selected a scaling method, you can choose to manually | |
| 639 specify the minimum and maximum expected values, or you can let JiG | |
| 640 determine them for you automatically. | |
| 641 | |
| 642 Finally, opacity is the only mapping we currently provide. Future | |
| 643 iterations will attempt to improve upon this and provide more colour | |
| 644 scales. The Opacity option maps the highest scoring features to full | |
| 645 opacity, and everything else to lower ones. | |
| 646 | |
| 647 BAM Pileups | |
| 648 ~~~~~~~~~~~ | |
| 649 | |
| 650 We support BAM files and can automatically generate SNP tracks based on | |
| 651 that bam data. | |
| 652 | |
| 653 .. image:: bam.png | |
| 654 | |
| 655 This is *strongly discouraged* for high coverage density datasets. | |
| 656 Unfortunately there are no other configuration options exposed for bam | |
| 657 files. If you find JBrowse options you wish to see exposed, please let | |
| 658 `me <mailto:esr+jig@tamu.edu>`__ know. | |
| 659 | |
| 660 BlastXML | |
| 661 ~~~~~~~~ | |
| 662 | |
| 663 .. image:: blast.png | |
| 664 | |
| 665 JiG now supports both blastn and blastp datasets. JiG internally uses a | |
| 666 blastXML to gapped GFF3 tool to convert your blastxml datasets into a | |
| 667 format amenable to visualization in JBrowse. This tool is also | |
| 668 available separately from the IUC on the toolshed. | |
| 669 | |
| 670 **Minimum Gap Size** reflects how long a gap must be before it becomes a | |
| 671 real gap in the processed gff3 file. In the picture above, various sizes | |
| 672 of gaps can be seen. If the minimum gap size was set much higher, say | |
| 673 100nt, many of the smaller gaps would disappear, and the features on | |
| 674 both sides would be merged into one, longer feature. This setting is | |
| 675 inversely proportional to runtime and output file size. *Do not set this | |
| 676 to a low value for large datasets*. By setting this number lower, you | |
| 677 will have extremely large outputs and extremely long runtimes. The | |
| 678 default was configured based off of the author's experience, but the | |
| 679 author only works on small viruses. It is *strongly* recommended that | |
| 680 you filter your blast results before display, e.g. picking out the top | |
| 681 10 hits or so. | |
| 682 | |
| 683 **Protein blast search** option merely informs underlying tools that | |
| 684 they should adjust feature locations by 3x. | |
| 685 | |
| 686 Styling Options | |
| 687 ^^^^^^^^^^^^^^^ | |
| 688 | |
| 689 Please see the styling options for GFF3 datasets, they are identical. | |
| 690 | |
| 691 Feature Score Scaling & Coloring Options | |
| 692 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 693 | |
| 694 Please see the score scaling and colouring options for GFF3 datasets, | |
| 695 they are identical. Remember to set your score scaling to "blast" method | |
| 696 if you do use it. | |
| 697 | |
| 698 Bigwig XY | |
| 699 ~~~~~~~~~ | |
| 700 | |
| 701 .. image:: bigwig.png | |
| 702 | |
| 703 **XYPlot** | |
| 704 | |
| 705 BigWig tracks can be displayed as a "density" plot which is continuous | |
| 706 line which varies in colour, or as an "XYplot." XYplots are preferable | |
| 707 for users to visually identify specific features in a bigwig track, | |
| 708 however density tracks are more visually compact. | |
| 709 | |
| 710 **Variance Band** is an option available to XYPlots, and can be seen in | |
| 711 the third and fourth tracks in the above picture. This overlays a mean | |
| 712 line, and 1 and 2 standard deviation areas. | |
| 713 | |
| 714 **Track Scaling** is different from colour scaling, instead it | |
| 715 configures how the track behaves inside of JBrowse. **Autoscaling | |
| 716 globally** means that JBrowse will determine the minimum and maximum for | |
| 717 the track, and fix the bounds of the viewport to that. E.g. if your | |
| 718 track ranges from 1-1000, and the region you're currently zoomed to only | |
| 719 goes from 0-50, then the viewport range will still show 1-1000. This is | |
| 720 good for global genomic context. However you may wish to consider | |
| 721 **autoscaling locally** instead. In the example of a region which varies | |
| 722 from 0-50, autoscaling locally would cause the individual track's | |
| 723 viewport to re-adjust and show just the 0-50 region. If neither of these | |
| 724 options are palatable, you may manually hardcode the minimum and | |
| 725 maximums for the track to scale to. | |
| 726 | |
| 727 Colour Options | |
| 728 ^^^^^^^^^^^^^^ | |
| 729 | |
| 730 BigWig tracks have two colours in JBrowse, a positive and a negative | |
| 731 colour. | |
| 732 | |
| 733 As always you may manually choose a colour, or let JiG choose for you. | |
| 734 | |
| 735 One of the more interesting options is the **Bicolor pivot**. This | |
| 736 option allows you to control the point at which JBrowse switches from | |
| 737 the positive colour to the negative. In the above graphic, you can see | |
| 738 this has been configured to "mean" for the first two (orange and blue) | |
| 739 tracks. | |
| 740 | |
| 741 VCFs/SNPs | |
| 742 ~~~~~~~~~ | |
| 743 | |
| 744 These tracks do not support any special configuration. | |
| 745 | |
| 746 Known Issues | |
| 747 ------------ | |
| 748 | |
| 749 - More than 30 landmark features cannot be listed in the manual | |
| 750 selector. | |
| 751 - Non GFF3 likely has issue with automatically determined min/max | |
| 752 scores. Manually specify minimum and maximum score attributes, or do | |
| 753 not use varied colours based on scores to avoid this issue. | |
| 754 | |
|
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756 @ATTRIBUTION@ |
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757 ]]></help> |
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758 <citations> |
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759 <citation type="doi">10.1101/gr.094607.109</citation> |
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760 </citations> |
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761 </tool> |
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762 |