Mercurial > repos > iuc > jbrowse
annotate jbrowse.xml @ 5:ae9382cfb6ac draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 15:06:43 -0400 |
| parents | 7342f467507b |
| children | ecbdfc775b9a |
| rev | line source |
|---|---|
|
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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1 <tool id="jbrowse" name="JBrowse" version="0.5"> |
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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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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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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
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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
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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
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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:
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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
parents:
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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:
3
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changeset
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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 $__tool_directory__/jbrowse.py | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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23 |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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changeset
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24 --jbrowse \${JBROWSE_SOURCE_DIR} |
| 3 | 25 #if str($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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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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75 #if str($action.genomes) != "None": |
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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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76 #for $genome in $action.genomes: |
| 3 | 77 <genome>$genome</genome> |
| 78 #end for | |
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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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79 #end if |
| 3 | 80 </genomes> |
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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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81 <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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82 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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83 <trackPadding>${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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84 |
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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 <shareLink>${jbgen.shareLink}</shareLink> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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86 <aboutDescription>${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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87 <show_tracklist>${jbgen.show_tracklist}</show_tracklist> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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88 <show_nav>${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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89 <show_overview>${jbgen.show_overview}</show_overview> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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90 <show_menu>${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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91 <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:
3
diff
changeset
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92 </general> |
| 3 | 93 </metadata> |
| 94 <tracks> | |
| 95 #for $tg in $track_groups: | |
| 96 #for $track in $tg.data_tracks: | |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
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97 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
| 3 | 98 <files> |
| 99 #for $dataset in $track.data_format.annotation: | |
| 100 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" /> | |
| 101 #end for | |
| 102 </files> | |
| 103 | |
| 104 <options> | |
| 105 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast": | |
| 106 <style> | |
| 107 <className>${track.data_format.jbstyle.style_classname}</className> | |
| 108 <description>${track.data_format.jbstyle.style_description}</description> | |
| 109 <label>${track.data_format.jbstyle.style_label}</label> | |
| 110 <height>${track.data_format.jbstyle.style_height}</height> | |
| 111 </style> | |
| 112 <scaling> | |
| 113 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none": | |
| 114 <method>ignore</method> | |
| 115 <scheme> | |
| 116 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic": | |
| 117 <color>__auto__</color> | |
| 118 #else | |
| 119 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color> | |
| 120 #end if | |
| 121 </scheme> | |
| 122 #else | |
| 123 <method>score</method> | |
| 124 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo> | |
| 125 <scales> | |
| 126 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type> | |
| 127 | |
| 128 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual": | |
| 129 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min> | |
| 130 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max> | |
| 131 #end if | |
| 132 </scales> | |
| 133 <scheme> | |
| 134 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type> | |
| 135 ## auto_color | |
| 136 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity": | |
| 137 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic": | |
| 138 <color>__auto__</color> | |
| 139 #else | |
| 140 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color> | |
| 141 #end if | |
| 142 #end if | |
| 143 </scheme> | |
| 144 #end if | |
| 145 </scaling> | |
| 146 #end if | |
| 147 | |
| 148 #if str($track.data_format.data_format_select) == "wiggle": | |
| 149 <wiggle> | |
| 150 <type>${track.data_format.xyplot}</type> | |
| 151 <variance_band>${track.data_format.var_band}</variance_band> | |
| 152 #if str($track.data_format.scaling.scale_select) == "auto_local": | |
| 153 <autoscale>local</autoscale> | |
| 154 #else if str($track.data_format.scaling.scale_select) == "auto_global": | |
| 155 <autoscale>global</autoscale> | |
| 156 #else: | |
| 157 <min>${track.data_format.scaling.minimum}</min> | |
| 158 <max>${track.data_format.scaling.maximum}</max> | |
| 159 #end if | |
| 160 | |
| 161 ## Wiggle tracks need special color config | |
| 162 #if str($track.data_format.jbcolor.color.color_select) != "automatic": | |
| 163 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos> | |
| 164 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg> | |
| 165 #else: | |
| 166 <color_pos>__auto__</color_pos> | |
| 167 <color_neg>__auto__</color_neg> | |
| 168 #end if | |
| 169 | |
| 170 ## Bicolor pivot config | |
| 171 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero": | |
| 172 <bicolor_pivot>zero</bicolor_pivot> | |
| 173 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean": | |
| 174 <bicolor_pivot>mean</bicolor_pivot> | |
| 175 #else: | |
| 176 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot> | |
| 177 #end if | |
| 178 </wiggle> | |
| 179 #else if str($track.data_format.data_format_select) == "pileup": | |
| 180 <pileup> | |
| 181 <auto_snp>${track.data_format.auto_snp}</auto_snp> | |
| 182 <bam_indices> | |
| 183 #for $dataset in $track.data_format.annotation: | |
| 184 <bam_index>${dataset.metadata.bam_index}</bam_index> | |
| 185 #end for | |
| 186 </bam_indices> | |
| 187 </pileup> | |
| 188 #else if str($track.data_format.data_format_select) == "blast": | |
| 189 <blast> | |
| 190 #if str($track.data_format.blast_parent) != "": | |
| 191 <parent>${track.data_format.blast_parent}</parent> | |
| 192 #end if | |
| 193 <protein>${track.data_format.is_protein}</protein> | |
| 194 <min_gap>${track.data_format.min_gap}</min_gap> | |
| 195 </blast> | |
| 196 #else if str($track.data_format.data_format_select) == "gene_calls": | |
| 197 <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
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198 <trackType>${track.data_format.track_class}</trackType> |
| 3 | 199 #if $track.data_format.match_part.match_part_select: |
| 200 <match>${track.data_format.match_part.name}</match> | |
| 201 #end if | |
| 202 </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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203 ## #else if str($track.data_format.data_format_select) == "sparql": |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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204 ## <sparql> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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205 ## <url>${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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206 ## <label>${track.data_format.label}</label> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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207 ## <!-- This is going to be an absolutey nightmare --> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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208 ## <query>${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
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209 ## </sparql> |
| 3 | 210 #end if |
| 211 </options> | |
| 212 </track> | |
| 213 #end for | |
| 214 #end for | |
| 215 </tracks> | |
| 216 </root> | |
| 217 ]]> | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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218 </configfile> |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
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219 </configfiles> |
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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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220 <inputs> |
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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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221 <conditional name="action" label="Action"> |
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222 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> |
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223 <option value="create">New JBrowse Instance</option> |
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224 <option value="update">Update exising JBrowse Instance</option> |
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225 </param> |
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226 <when value="create"> |
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227 <param label="Fasta Sequence(s)" |
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228 name="genomes" |
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229 type="data" |
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230 format="fasta" |
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231 multiple="True"/> |
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232 </when> |
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233 <when value="update"> |
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234 <param label="Additional Fasta Sequence(s)" |
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235 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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236 name="genomes" |
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237 type="data" |
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238 format="fasta" |
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239 optional="True" |
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240 multiple="True"/> |
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241 <param label="Previous JBrowse Instance" |
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242 name="update_jbrowse" |
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243 type="data" |
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244 format="html" /> |
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245 </when> |
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246 </conditional> |
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247 |
| 3 | 248 <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"/> |
| 249 | |
| 250 <param label="Genetic Code" name="gencode" type="select"> | |
| 251 <option value="1">1. The Standard Code</option> | |
| 252 <option value="2">2. The Vertebrate Mitochondrial Code</option> | |
| 253 <option value="3">3. The Yeast Mitochondrial Code</option> | |
| 254 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
| 255 <option value="5">5. The Invertebrate Mitochondrial Code</option> | |
| 256 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
| 257 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option> | |
| 258 <option value="10">10. The Euplotid Nuclear Code</option> | |
| 259 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option> | |
| 260 <option value="12">12. The Alternative Yeast Nuclear Code</option> | |
| 261 <option value="13">13. The Ascidian Mitochondrial Code</option> | |
| 262 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option> | |
| 263 <option value="16">16. Chlorophycean Mitochondrial Code</option> | |
| 264 <option value="21">21. Trematode Mitochondrial Code</option> | |
| 265 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option> | |
| 266 <option value="23">23. Thraustochytrium Mitochondrial Code</option> | |
| 267 <option value="24">24. Pterobranchia Mitochondrial Code</option> | |
| 268 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> | |
| 269 </param> | |
| 270 | |
| 271 <repeat name="track_groups" title="Track Group"> | |
| 272 <param label="Track Category" | |
| 273 name="category" | |
| 274 type="text" | |
| 275 value="Default" | |
| 276 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/> | |
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277 <repeat name="data_tracks" title="Annotation Track"> |
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278 <conditional name="data_format" label="Track Options"> |
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279 <param type="select" label="Track Type" name="data_format_select"> |
| 3 | 280 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> |
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281 <option value="pileup">BAM Pileups</option> |
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282 <option value="blast">Blast XML</option> |
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283 <option value="wiggle">BigWig XY</option> |
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284 <option value="vcf">VCF SNPs</option> |
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285 <!--<option value="sparql">SPARQL</option>--> |
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286 </param> |
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287 <when value="blast"> |
| 3 | 288 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> |
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289 |
| 3 | 290 <param label="Features used in Blast Search" |
| 291 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." | |
| 292 format="gff3" | |
| 293 name="blast_parent" | |
| 294 optional="true" | |
| 295 type="data"/> | |
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296 |
| 3 | 297 <param label="Minimum Gap Size" |
| 298 help="before a new match_part feature is created" | |
| 299 name="min_gap" | |
| 300 type="integer" | |
| 301 value="10" | |
| 302 min="2" /> | |
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303 <param label="Is this a protein blast search?" |
| 3 | 304 type="boolean" |
| 305 name="is_protein" | |
| 306 truevalue="true" | |
| 307 falsevalue="false" /> | |
| 308 | |
| 309 <expand macro="track_styling" | |
| 310 classname="feature" | |
| 311 label="description" | |
| 312 description="Hit_titles" | |
| 313 height="600px"/> | |
| 314 <expand macro="color_selection" | |
| 315 token_scaling_lin_select="false" | |
| 316 token_scaling_log_select="true" /> | |
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317 <expand macro="track_display" /> |
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318 </when> |
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319 <when value="vcf"> |
| 3 | 320 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> |
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321 <expand macro="track_display" /> |
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322 </when> |
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323 <when value="gene_calls"> |
| 3 | 324 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> |
| 325 <conditional name="match_part" label="match/match_part data"> | |
| 326 <param label="This is match/match_part data" | |
| 327 type="boolean" | |
| 328 name="match_part_select" | |
| 329 truevalue="true" | |
| 330 falsevalue="false" /> | |
| 331 <when value="true"> | |
| 332 <param label="Match Part Feature Type" | |
| 333 name="name" | |
| 334 type="text" | |
| 335 value="match" | |
| 336 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" | |
| 337 optional="False"/> | |
| 338 </when> | |
| 339 <when value="false" /> | |
| 340 </conditional> | |
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341 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> |
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342 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> |
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343 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> |
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344 </param> |
| 3 | 345 <expand macro="track_styling" /> |
| 346 <expand macro="color_selection" /> | |
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347 <expand macro="track_display" /> |
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348 </when> |
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349 <when value="pileup"> |
| 3 | 350 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
| 351 <param label="Autogenerate SNP Track" | |
| 352 help="Not recommended for deep coverage BAM files" | |
| 353 type="boolean" | |
| 354 name="auto_snp" | |
| 355 truevalue="true" | |
| 356 falsevalue="false" /> | |
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357 <expand macro="track_display" /> |
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358 </when> |
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359 <when value="wiggle"> |
| 3 | 360 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
| 361 | |
| 362 <param label="Use XYPlot" | |
| 363 help="instead of continuous colored band" | |
| 364 type="boolean" | |
| 365 name="xyplot" | |
| 366 truevalue="JBrowse/View/Track/Wiggle/XYPlot" | |
| 367 falsevalue="JBrowse/View/Track/Wiggle/Density" /> | |
| 368 <param label="Show variance band" | |
| 369 help="Only for XYPlots" | |
| 370 type="boolean" | |
| 371 name="var_band" | |
| 372 truevalue="true" | |
| 373 falsevalue="false" /> | |
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374 |
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375 <conditional name="scaling" label="Scaling"> |
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376 <param type="select" label="Track Scaling" name="scale_select"> |
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377 <option value="auto_local">Autoscale (local)</option> |
| 3 | 378 <option value="auto_global" selected="true">Autoscale (global)</option> |
| 379 <option value="fixed">Specify Min/Max</option> | |
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380 </param> |
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381 <when value="auto_local"></when> |
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382 <when value="auto_global"></when> |
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383 <when value="fixed"> |
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384 <param label="Track minimum" name="minimum" |
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385 type="integer" value="0" /> |
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386 <param label="Track maximum" name="maximum" |
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387 type="integer" value="100" /> |
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388 </when> |
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389 </conditional> |
| 3 | 390 <expand macro="color_selection_minmax" /> |
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391 <expand macro="track_display" /> |
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392 </when> |
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393 <!-- |
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394 <when value="sparql"> |
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395 <param type="text" label="SPARQL Server URL" name="url" /> |
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396 <param type="text" label="Track Label" name="key" value="SPARQL Genes" /> |
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397 <param type="text" label="SPARQL Query" name="query" area="true" /> |
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398 <expand macro="track_display" /> |
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399 </when> |
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400 --> |
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401 </conditional> |
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402 </repeat> |
| 3 | 403 </repeat> |
| 404 | |
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405 <expand macro="general_options" /> |
| 3 | 406 <param type="hidden" name="uglyTestingHack" value="" /> |
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407 </inputs> |
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408 <outputs> |
| 3 | 409 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/> |
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410 </outputs> |
| 3 | 411 <tests> |
| 412 <test> | |
| 413 <!-- gencode --> | |
| 414 <param name="genomes" value="merlin.fa"/> | |
| 415 <param name="gencode" value="1" /> | |
| 416 <param name="standalone" value="Data Directory" /> | |
| 417 <param name="uglyTestingHack" value="enabled" /> | |
| 418 <output name="output" file="gencode/test-1.xml" lines_diff="4" /> | |
| 419 </test> | |
| 420 <test> | |
| 421 <param name="genomes" value="merlin.fa"/> | |
| 422 <param name="gencode" value="11" /> | |
| 423 <param name="standalone" value="Data Directory" /> | |
| 424 <param name="uglyTestingHack" value="enabled" /> | |
| 425 <output name="output" file="gencode/test.xml" lines_diff="4"/> | |
| 426 </test> | |
| 427 <!-- | |
| 428 <test> | |
| 429 <param name="genomes" value="merlin.fa"/> | |
| 430 <param name="gencode" value="11" /> | |
| 431 <param name="standalone" value="Data Directory" /> | |
| 432 <param name="track_groups_0|category" value="Auto Coloured" /> | |
| 433 <param name="track_groups_0|data_tracks_0|data_format" value="gene_calls"/> | |
| 434 <param name="track_groups_0|data_tracks_0|annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> | |
| 435 <param name="track_groups_0|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 436 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 437 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> | |
| 438 | |
| 439 | |
| 440 <param name="track_groups_1|category" value="Ignore Scale" /> | |
| 441 <param name="track_groups_1|data_tracks_0|data_format" value="gene_calls"/> | |
| 442 <param name="track_groups_1|data_tracks_0|annotation" value="gff3/1.gff"/> | |
| 443 <param name="track_groups_1|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 444 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 445 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|color_select" value="manual"/> | |
| 446 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|style_color" value="#ff00ff"/> | |
| 447 | |
| 448 <param name="track_groups_2|category" value="Scaled Colour" /> | |
| 449 <param name="track_groups_2|data_tracks_0|data_format" value="gene_calls"/> | |
| 450 <param name="track_groups_2|data_tracks_0|annotation" value="gff3/1.gff"/> | |
| 451 <param name="track_groups_2|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 452 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 453 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 454 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 455 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 456 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> | |
| 457 <param name="track_groups_2|data_tracks_1|data_format" value="gene_calls"/> | |
| 458 <param name="track_groups_2|data_tracks_1|annotation" value="gff3/1.gff"/> | |
| 459 <param name="track_groups_2|data_tracks_1|match_part|match_part_select" value="false"/> | |
| 460 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 461 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 462 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 463 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 464 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> | |
| 465 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|style_color" value="#0000ff"/> | |
| 466 <param name="track_groups_2|data_tracks_2|data_format" value="gene_calls"/> | |
| 467 <param name="track_groups_2|data_tracks_2|annotation" value="gff3/1.gff"/> | |
| 468 <param name="track_groups_2|data_tracks_2|match_part|match_part_select" value="false"/> | |
| 469 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 470 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 471 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 472 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|minimum" value="0"/> | |
| 473 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> | |
| 474 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 475 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> | |
| 476 <param name="track_groups_2|data_tracks_3|data_format" value="gene_calls"/> | |
| 477 <param name="track_groups_2|data_tracks_3|annotation" value="gff3/1.gff"/> | |
| 478 <param name="track_groups_2|data_tracks_3|match_part|match_part_select" value="false"/> | |
| 479 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 480 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 481 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 482 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|minimum" value="0"/> | |
| 483 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> | |
| 484 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 485 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> | |
| 486 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|style_color" value="#ff0000"/> | |
| 487 | |
| 488 <param name="track_groups_3|category" value="Realistic" /> | |
| 489 <param name="track_groups_3|data_tracks_0|data_format" value="gene_calls"/> | |
| 490 <param name="track_groups_3|data_tracks_0|annotation" value="gff3/interpro.gff"/> | |
| 491 <param name="track_groups_3|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 492 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 493 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> | |
| 494 <param name="track_groups_3|data_tracks_1|data_format" value="gene_calls"/> | |
| 495 <param name="track_groups_3|data_tracks_1|annotation" value="gff3/2.gff"/> | |
| 496 <param name="track_groups_3|data_tracks_1|match_part|match_part_select" value="true"/> | |
| 497 <param name="track_groups_3|data_tracks_1|match_part|name" value="cDNA_match"/> | |
| 498 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 499 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color|color_select" value="automatic"/> | |
| 500 | |
| 501 <param name="uglyTestingHack" value="enabled" /> | |
| 502 <output name="output" file="gff3/test.xml" /> | |
| 503 </test> | |
| 504 --> | |
| 505 </tests> | |
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506 <help><![CDATA[ |
| 3 | 507 JBrowse-in-Galaxy |
| 508 ================= | |
| 509 | |
| 510 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible | |
| 511 alternative to Trackster. | |
| 512 | |
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513 Overview |
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514 -------- |
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515 |
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516 JBrowse is a fast, embeddable genome browser built completely with |
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517 JavaScript and HTML5. |
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518 |
| 3 | 519 The JBrowse-in-Galaxy (JiG) tool was written to help build complex |
| 520 JBrowse installations straight from Galaxy, taking advantage of the | |
| 521 latest Galaxy features such as dataset collections, sections, and colour | |
| 522 pickers. It allows you to build up a JBrowse instance without worrying | |
| 523 about how to run the command line tools to format your data, and which | |
| 524 options need to be supplied and where. Additionally it comes with many | |
| 525 javascript functions to handle colouring of features which would be | |
| 526 nearly impossible to write without the assistance of this tool. | |
| 527 | |
| 528 The JBrowse-in-Galaxy tool is maintained by `Eric | |
| 529 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you | |
| 530 encounter missing features or bugs. | |
| 531 | |
| 532 Options | |
| 533 ------- | |
| 534 | |
| 535 The first option you encounter is the **Fasta Sequence(s)**. This option | |
| 536 now accepts multiple fasta files, allowing you to build JBrowse | |
| 537 instances that contain data for multiple genomes or chrosomomes | |
| 538 (generally known as "landmark features" in gff3 terminology.) Up to 30 | |
| 539 will be shown from the dropdown selector within JBrowse, this is a known | |
| 540 issue. | |
| 541 | |
| 542 **Standalone Instances** are a somewhat in-development feature. | |
| 543 Currently Galaxy copies the entire JBrowse directory in order to have a | |
| 544 complete, downloadable file that contains a ready-to-go JBrowse | |
| 545 instance. This is obviously an anti-feature because users don't want a | |
| 546 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse | |
| 547 dataset in their history, and admins don't want useless copies of | |
| 548 JBrowse on disk. Unfortunately we have not come up with the perfect | |
| 549 solution just yet, but we're working on it! In the meantime, users have | |
| 550 been given the option to produce just the ``data/`` directory. For those | |
| 551 unfamiliar with JBrowse, the ``data/`` directory contains processed data | |
| 552 files, but no way to view them. This feature is additionally implemented | |
| 553 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration. | |
| 554 | |
| 555 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse, | |
| 556 which allows users to specify a non standard genetic code, and have | |
| 557 JBrowse highlight the correct start and stop codons. If you would like | |
| 558 to use a coding table not provided by this list, please let | |
| 559 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for | |
| 560 this. | |
| 561 | |
| 562 **Track Groups** represent a set of tracks in a single category. These | |
| 563 can be used to let your users understand relationships between large | |
| 564 groups of tracks. | |
| 565 | |
| 566 .. image:: sections.png | |
| 567 | |
| 568 Annotation Tracks | |
| 569 ----------------- | |
| 570 | |
| 571 Within Track Groups, you have one or more **Annotation Tracks**. Each | |
| 572 Annotation Track is a groups of datasets which have similar styling. | |
| 573 This allows you to rapidly build up JBrowse instances without having to | |
| 574 configure tracks individually. A massive improvement over previous | |
| 575 versions. For example, if you have five different GFF3 files from | |
| 576 various gene callers that you wish to display, you can take advantage of | |
| 577 this feature to style all of them similarly. | |
| 578 | |
| 579 There are a few different types of tracks supported, each with their own | |
| 580 set of options: | |
| 581 | |
| 582 GFF3/BED/GBK | |
| 583 ~~~~~~~~~~~~ | |
| 584 | |
| 585 These are your standard feature tracks. They usually highlight genes, | |
| 586 mRNAs and other features of interest along a genomic region. The | |
| 587 underlying tool and this help documentation focus primarily on GFF3 | |
| 588 data, and have not been tested extensively with other formats. Automatic | |
| 589 min/max detection will likely fail under BED and GBK datasets. | |
| 590 | |
| 591 The data may be of a subclass we call **match/match part** data. This | |
| 592 consists of top level ``match`` features, with a child ``match_part`` | |
| 593 feature, and is often used in displaying alignments. (See "Alignments" | |
| 594 section on the `GFF3 | |
| 595 specification <http://www.sequenceontology.org/gff3.shtml>`__ for more | |
| 596 information). If the data is match/match part, you will need to specify | |
| 597 the top level match feature name, as it can be one of a few different SO | |
| 598 terms, and JiG does not yet have the ability to understand SO terms. | |
| 599 | |
| 600 Next up is the **Styling Options** section, which lets you control a few | |
| 601 properties on how the track is styled. Most of these you will not need | |
| 602 to configure and can safely leave on defaults. Occasionally you will | |
| 603 want to change what information is shown in the end product. | |
| 604 | |
| 605 .. image:: styling.png | |
| 606 | |
| 607 In the above image you can see some black text, and some blue text. The | |
| 608 source of the black text is configured with the **style.label** option, | |
| 609 and the source of the blue text is configured with the | |
| 610 **style.description** option. | |
| 611 | |
| 612 Feature Score Scaling & Colouring Options | |
| 613 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 614 | |
| 615 First, you need to choose between ignoring the score attribute of GFF3 | |
| 616 files, or using it. If you choose to ignore it, all features will be | |
| 617 coloured with a solid colour. If you choose to use it, features will | |
| 618 have slightly different colours based on their scores. | |
| 619 | |
| 620 .. image:: opacity.png | |
| 621 | |
| 622 If you choose **Ignore score**, you may choose between automatically | |
| 623 choosing a colour, or manually specifying one. The automatically chosen | |
| 624 colours vary along a brewer palette and generally look quite nice with | |
| 625 no human intervention required. The manual colour choice is somewhat | |
| 626 self explanatory. Clicking on the small coloured square will bring up a | |
| 627 colour palette. | |
| 628 | |
| 629 If you choose **Base on score**, you're faced with a dizzying array of | |
| 630 options. First is the function to map the colour choices to colour | |
| 631 values. JiG comes with a few functions built in such as linear scaling, | |
| 632 logarithmic scaling, and blast scaling. | |
| 633 | |
| 634 The **linear scaling** method says "take these values, and they map | |
| 635 directly to a range of output values". **Logarithmic scaling** says | |
| 636 "please take the log of the score before mapping", and **Blast scaling** | |
| 637 is further specialised to handle blast data more nicely. These are | |
| 638 convenience functions to help transform the wide array of possible | |
| 639 values in the GFF3 score attribute to more meaningful numbers. If you | |
| 640 need more comprehensive score scaling, it is recommended that you | |
| 641 pre-process your GFF3 files somehow. | |
| 642 | |
| 643 Once you've selected a scaling method, you can choose to manually | |
| 644 specify the minimum and maximum expected values, or you can let JiG | |
| 645 determine them for you automatically. | |
| 646 | |
| 647 Finally, opacity is the only mapping we currently provide. Future | |
| 648 iterations will attempt to improve upon this and provide more colour | |
| 649 scales. The Opacity option maps the highest scoring features to full | |
| 650 opacity, and everything else to lower ones. | |
| 651 | |
| 652 BAM Pileups | |
| 653 ~~~~~~~~~~~ | |
| 654 | |
| 655 We support BAM files and can automatically generate SNP tracks based on | |
| 656 that bam data. | |
| 657 | |
| 658 .. image:: bam.png | |
| 659 | |
| 660 This is *strongly discouraged* for high coverage density datasets. | |
| 661 Unfortunately there are no other configuration options exposed for bam | |
| 662 files. If you find JBrowse options you wish to see exposed, please let | |
| 663 `me <mailto:esr+jig@tamu.edu>`__ know. | |
| 664 | |
| 665 BlastXML | |
| 666 ~~~~~~~~ | |
| 667 | |
| 668 .. image:: blast.png | |
| 669 | |
| 670 JiG now supports both blastn and blastp datasets. JiG internally uses a | |
| 671 blastXML to gapped GFF3 tool to convert your blastxml datasets into a | |
| 672 format amenable to visualization in JBrowse. This tool is also | |
| 673 available separately from the IUC on the toolshed. | |
| 674 | |
| 675 **Minimum Gap Size** reflects how long a gap must be before it becomes a | |
| 676 real gap in the processed gff3 file. In the picture above, various sizes | |
| 677 of gaps can be seen. If the minimum gap size was set much higher, say | |
| 678 100nt, many of the smaller gaps would disappear, and the features on | |
| 679 both sides would be merged into one, longer feature. This setting is | |
| 680 inversely proportional to runtime and output file size. *Do not set this | |
| 681 to a low value for large datasets*. By setting this number lower, you | |
| 682 will have extremely large outputs and extremely long runtimes. The | |
| 683 default was configured based off of the author's experience, but the | |
| 684 author only works on small viruses. It is *strongly* recommended that | |
| 685 you filter your blast results before display, e.g. picking out the top | |
| 686 10 hits or so. | |
| 687 | |
| 688 **Protein blast search** option merely informs underlying tools that | |
| 689 they should adjust feature locations by 3x. | |
| 690 | |
| 691 Styling Options | |
| 692 ^^^^^^^^^^^^^^^ | |
| 693 | |
| 694 Please see the styling options for GFF3 datasets, they are identical. | |
| 695 | |
| 696 Feature Score Scaling & Coloring Options | |
| 697 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 698 | |
| 699 Please see the score scaling and colouring options for GFF3 datasets, | |
| 700 they are identical. Remember to set your score scaling to "blast" method | |
| 701 if you do use it. | |
| 702 | |
| 703 Bigwig XY | |
| 704 ~~~~~~~~~ | |
| 705 | |
| 706 .. image:: bigwig.png | |
| 707 | |
| 708 **XYPlot** | |
| 709 | |
| 710 BigWig tracks can be displayed as a "density" plot which is continuous | |
| 711 line which varies in colour, or as an "XYplot." XYplots are preferable | |
| 712 for users to visually identify specific features in a bigwig track, | |
| 713 however density tracks are more visually compact. | |
| 714 | |
| 715 **Variance Band** is an option available to XYPlots, and can be seen in | |
| 716 the third and fourth tracks in the above picture. This overlays a mean | |
| 717 line, and 1 and 2 standard deviation areas. | |
| 718 | |
| 719 **Track Scaling** is different from colour scaling, instead it | |
| 720 configures how the track behaves inside of JBrowse. **Autoscaling | |
| 721 globally** means that JBrowse will determine the minimum and maximum for | |
| 722 the track, and fix the bounds of the viewport to that. E.g. if your | |
| 723 track ranges from 1-1000, and the region you're currently zoomed to only | |
| 724 goes from 0-50, then the viewport range will still show 1-1000. This is | |
| 725 good for global genomic context. However you may wish to consider | |
| 726 **autoscaling locally** instead. In the example of a region which varies | |
| 727 from 0-50, autoscaling locally would cause the individual track's | |
| 728 viewport to re-adjust and show just the 0-50 region. If neither of these | |
| 729 options are palatable, you may manually hardcode the minimum and | |
| 730 maximums for the track to scale to. | |
| 731 | |
| 732 Colour Options | |
| 733 ^^^^^^^^^^^^^^ | |
| 734 | |
| 735 BigWig tracks have two colours in JBrowse, a positive and a negative | |
| 736 colour. | |
| 737 | |
| 738 As always you may manually choose a colour, or let JiG choose for you. | |
| 739 | |
| 740 One of the more interesting options is the **Bicolor pivot**. This | |
| 741 option allows you to control the point at which JBrowse switches from | |
| 742 the positive colour to the negative. In the above graphic, you can see | |
| 743 this has been configured to "mean" for the first two (orange and blue) | |
| 744 tracks. | |
| 745 | |
| 746 VCFs/SNPs | |
| 747 ~~~~~~~~~ | |
| 748 | |
| 749 These tracks do not support any special configuration. | |
| 750 | |
| 751 Known Issues | |
| 752 ------------ | |
| 753 | |
| 754 - More than 30 landmark features cannot be listed in the manual | |
| 755 selector. | |
| 756 - Non GFF3 likely has issue with automatically determined min/max | |
| 757 scores. Manually specify minimum and maximum score attributes, or do | |
| 758 not use varied colours based on scores to avoid this issue. | |
| 759 | |
|
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760 |
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761 @ATTRIBUTION@ |
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762 ]]></help> |
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763 <citations> |
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764 <citation type="doi">10.1101/gr.094607.109</citation> |
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765 </citations> |
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766 </tool> |
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767 |