Mercurial > repos > iuc > jbrowse
annotate jbrowse.xml @ 16:b5c5470d7c09 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
| author | iuc |
|---|---|
| date | Wed, 13 Sep 2017 13:07:20 -0400 |
| parents | 69c5e9c0add0 |
| children | ff11d442feed |
| rev | line source |
|---|---|
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16
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
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changeset
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1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.2"> |
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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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diff
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:
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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
parents:
diff
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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7 <expand macro="stdio"/> |
| 3 | 8 <command><![CDATA[ |
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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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9 |
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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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10 #if $action.action_select == "create": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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11 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
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12 #else: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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13 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
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14 #end if |
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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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15 |
| 3 | 16 ## Copy the XML file into the directory, mostly for debugging |
| 17 ## but nice if users want to reproduce locally | |
| 18 cp $trackxml $output.files_path/galaxy.xml && | |
| 19 | |
| 20 ## Once that's done, we run the python script to handle the real work | |
| 21 python $__tool_directory__/jbrowse.py | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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22 |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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23 --jbrowse \${JBROWSE_SOURCE_DIR} |
| 3 | 24 #if str($standalone) == "Complete": |
| 25 --standalone | |
| 26 #end if | |
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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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27 |
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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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28 --outdir $output.files_path |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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29 $trackxml && |
| 3 | 30 |
| 31 #if str($standalone) == "Complete": | |
| 32 mv $output.files_path/index.html $output; | |
| 33 #else: | |
| 34 mv $dummyIndex $output; | |
| 35 #end if | |
| 36 | |
| 37 | |
| 38 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. | |
| 39 #if str($uglyTestingHack) == "enabled": | |
| 40 mv $trackxml $output | |
| 41 #end if | |
| 42 ]]></command> | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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43 <configfiles> |
| 3 | 44 <configfile name="dummyIndex"> |
| 45 <![CDATA[ | |
| 46 <html> | |
| 47 <head> | |
| 48 </head> | |
| 49 <body> | |
| 50 <h1>JBrowse Data Directory</h1> | |
| 51 <p> | |
| 52 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?) | |
| 53 started shipping with the ability to produce just the | |
| 54 "data" directory from a JBrowse instance, rather than a | |
| 55 complete, standalone instance. This was intended to be used | |
| 56 with the in-development Apollo integration, but may have other | |
| 57 uses as well. | |
| 58 </p> | |
| 59 <p> | |
| 60 <u>This is not usable on its own</u>. The output dataset may be | |
| 61 used with Apollo, or may be passed through the "JBrowse - | |
| 62 Convert to Standalone" tool in Galaxy to "upgrade" to a full | |
| 63 JBrowse instance. | |
| 64 </p> | |
| 65 </body> | |
| 66 </html> | |
| 67 ]]> | |
| 68 </configfile> | |
| 69 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> | |
| 70 <root> | |
| 71 <metadata> | |
| 72 <gencode>$gencode</gencode> | |
| 73 <genomes> | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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74 #if str($reference_genome.genome_type_select) == "indexed": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
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changeset
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75 <genome>${reference_genome.genomes.fields.path}</genome> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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76 #else |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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77 #for $genome in $reference_genome.genomes: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
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78 <genome>$genome</genome> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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79 #end for |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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80 #end if |
| 3 | 81 </genomes> |
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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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82 <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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83 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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84 <trackPadding>${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:
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85 |
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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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86 <shareLink>${jbgen.shareLink}</shareLink> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
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87 <aboutDescription>${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
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88 <show_tracklist>${jbgen.show_tracklist}</show_tracklist> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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89 <show_nav>${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
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90 <show_overview>${jbgen.show_overview}</show_overview> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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91 <show_menu>${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
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92 <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
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93 </general> |
| 3 | 94 </metadata> |
| 95 <tracks> | |
| 96 #for $tg in $track_groups: | |
| 97 #for $track in $tg.data_tracks: | |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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98 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
| 3 | 99 <files> |
| 100 #for $dataset in $track.data_format.annotation: | |
| 101 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" /> | |
| 102 #end for | |
| 103 </files> | |
| 104 | |
| 105 <options> | |
| 106 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast": | |
| 107 <style> | |
| 108 <className>${track.data_format.jbstyle.style_classname}</className> | |
| 109 <description>${track.data_format.jbstyle.style_description}</description> | |
| 110 <label>${track.data_format.jbstyle.style_label}</label> | |
| 111 <height>${track.data_format.jbstyle.style_height}</height> | |
| 112 </style> | |
| 113 <scaling> | |
| 114 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none": | |
| 115 <method>ignore</method> | |
| 116 <scheme> | |
| 117 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic": | |
| 118 <color>__auto__</color> | |
| 119 #else | |
| 120 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color> | |
| 121 #end if | |
| 122 </scheme> | |
| 123 #else | |
| 124 <method>score</method> | |
| 125 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo> | |
| 126 <scales> | |
| 127 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type> | |
| 128 | |
| 129 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual": | |
| 130 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min> | |
| 131 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max> | |
| 132 #end if | |
| 133 </scales> | |
| 134 <scheme> | |
| 135 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type> | |
| 136 ## auto_color | |
| 137 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity": | |
| 138 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic": | |
| 139 <color>__auto__</color> | |
| 140 #else | |
| 141 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color> | |
| 142 #end if | |
| 143 #end if | |
| 144 </scheme> | |
| 145 #end if | |
| 146 </scaling> | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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147 <menus> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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148 #for $menu_item in $track.data_format.jbmenu.track_menu: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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149 <menu> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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150 <action>${menu_item.menu_action}</action> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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151 #if str($menu_item.menu_label) != "": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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152 <label>${menu_item.menu_label}</label> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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153 #end if |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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154 #if str($menu_item.menu_title) != "": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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155 <title>${menu_item.menu_title}</title> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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156 #end if |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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157 #if str($menu_item.menu_url) != "": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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158 <url>${menu_item.menu_url.replace("&", "&").replace("\"", """)}</url> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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159 #end if |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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160 #if str($menu_item.menu_icon) != "": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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161 <iconClass>${menu_item.menu_icon}</iconClass> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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162 #end if |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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163 </menu> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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164 #end for |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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165 </menus> |
| 3 | 166 #end if |
| 167 | |
| 168 #if str($track.data_format.data_format_select) == "wiggle": | |
| 169 <wiggle> | |
| 170 <type>${track.data_format.xyplot}</type> | |
| 171 <variance_band>${track.data_format.var_band}</variance_band> | |
| 172 #if str($track.data_format.scaling.scale_select) == "auto_local": | |
| 173 <autoscale>local</autoscale> | |
| 174 #else if str($track.data_format.scaling.scale_select) == "auto_global": | |
| 175 <autoscale>global</autoscale> | |
| 176 #else: | |
| 177 <min>${track.data_format.scaling.minimum}</min> | |
| 178 <max>${track.data_format.scaling.maximum}</max> | |
| 179 #end if | |
| 180 | |
| 181 ## Wiggle tracks need special color config | |
| 182 #if str($track.data_format.jbcolor.color.color_select) != "automatic": | |
| 183 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos> | |
| 184 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg> | |
| 185 #else: | |
| 186 <color_pos>__auto__</color_pos> | |
| 187 <color_neg>__auto__</color_neg> | |
| 188 #end if | |
| 189 | |
| 190 ## Bicolor pivot config | |
| 191 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero": | |
| 192 <bicolor_pivot>zero</bicolor_pivot> | |
| 193 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean": | |
| 194 <bicolor_pivot>mean</bicolor_pivot> | |
| 195 #else: | |
| 196 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot> | |
| 197 #end if | |
| 198 </wiggle> | |
| 199 #else if str($track.data_format.data_format_select) == "pileup": | |
| 200 <pileup> | |
| 201 <auto_snp>${track.data_format.auto_snp}</auto_snp> | |
| 202 <bam_indices> | |
| 203 #for $dataset in $track.data_format.annotation: | |
| 204 <bam_index>${dataset.metadata.bam_index}</bam_index> | |
| 205 #end for | |
| 206 </bam_indices> | |
| 207 </pileup> | |
| 208 #else if str($track.data_format.data_format_select) == "blast": | |
| 209 <blast> | |
| 210 #if str($track.data_format.blast_parent) != "": | |
| 211 <parent>${track.data_format.blast_parent}</parent> | |
| 212 #end if | |
| 213 <protein>${track.data_format.is_protein}</protein> | |
| 214 <min_gap>${track.data_format.min_gap}</min_gap> | |
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215 <index>${track.data_format.index}</index> |
| 3 | 216 </blast> |
| 217 #else if str($track.data_format.data_format_select) == "gene_calls": | |
| 218 <gff> | |
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219 <trackType>${track.data_format.track_config.track_class}</trackType> |
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220 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures': |
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221 #if str($track.data_format.track_config.canvas_options.transcriptType) != "": |
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222 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType> |
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223 #end if |
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224 #if str($track.data_format.track_config.canvas_options.subParts) != "": |
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225 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts> |
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226 #end if |
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227 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false": |
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228 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs> |
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229 #end if |
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230 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures': |
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231 #if str($track.data_format.track_config.html_options.transcriptType) != "": |
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232 <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType> |
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233 #end if |
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234 #end if |
| 3 | 235 #if $track.data_format.match_part.match_part_select: |
| 236 <match>${track.data_format.match_part.name}</match> | |
| 237 #end if | |
|
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238 <index>${track.data_format.index}</index> |
| 3 | 239 </gff> |
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240 ## #else if str($track.data_format.data_format_select) == "sparql": |
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241 ## <sparql> |
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242 ## <url>${track.data_format.url}</url> |
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243 ## <label>${track.data_format.label}</label> |
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244 ## <!-- This is going to be an absolutey nightmare --> |
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245 ## <query>${track.data_format.query}</query> |
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246 ## </sparql> |
| 3 | 247 #end if |
| 248 </options> | |
| 249 </track> | |
| 250 #end for | |
| 251 #end for | |
| 252 </tracks> | |
| 253 </root> | |
|
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254 ]]></configfile> |
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255 </configfiles> |
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256 <inputs> |
|
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257 <conditional name="reference_genome"> |
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258 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> |
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259 <option selected="True" value="indexed">Use a built-in genome</option> |
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260 <option value="history">Use a genome from history</option> |
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261 </param> |
|
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262 <when value="indexed"> |
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263 <param |
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264 help="If your genome of interest is not listed, contact the Galaxy team" |
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265 label="Select a reference genome" |
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266 name="genomes" |
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267 type="select" |
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268 > |
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269 <options from_data_table="all_fasta"> |
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270 <filter column="2" type="sort_by" /> |
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271 <validator message="No genomes are available for the selected input dataset" type="no_options" /> |
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272 </options> |
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273 </param> |
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274 </when> |
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275 <when value="history"> |
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276 <param |
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277 format="fasta" |
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278 label="Select the reference genome" |
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279 name="genomes" |
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280 type="data" |
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281 multiple="True" /> |
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282 </when> |
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283 </conditional> |
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284 |
| 3 | 285 <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"/> |
| 286 | |
|
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287 |
| 3 | 288 <param label="Genetic Code" name="gencode" type="select"> |
| 289 <option value="1">1. The Standard Code</option> | |
| 290 <option value="2">2. The Vertebrate Mitochondrial Code</option> | |
| 291 <option value="3">3. The Yeast Mitochondrial Code</option> | |
| 292 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
| 293 <option value="5">5. The Invertebrate Mitochondrial Code</option> | |
| 294 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
| 295 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option> | |
| 296 <option value="10">10. The Euplotid Nuclear Code</option> | |
| 297 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option> | |
| 298 <option value="12">12. The Alternative Yeast Nuclear Code</option> | |
| 299 <option value="13">13. The Ascidian Mitochondrial Code</option> | |
| 300 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option> | |
| 301 <option value="16">16. Chlorophycean Mitochondrial Code</option> | |
| 302 <option value="21">21. Trematode Mitochondrial Code</option> | |
| 303 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option> | |
| 304 <option value="23">23. Thraustochytrium Mitochondrial Code</option> | |
| 305 <option value="24">24. Pterobranchia Mitochondrial Code</option> | |
| 306 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> | |
| 307 </param> | |
| 308 | |
|
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309 <conditional name="action"> |
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310 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> |
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311 <option value="create">New JBrowse Instance</option> |
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312 <option value="update">Update exising JBrowse Instance</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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313 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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314 <when value="create" /> |
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315 <when value="update"> |
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316 <param label="Previous JBrowse Instance" |
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317 name="update_jbrowse" |
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318 type="data" |
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319 format="html" /> |
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320 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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321 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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322 |
| 3 | 323 <repeat name="track_groups" title="Track Group"> |
| 324 <param label="Track Category" | |
| 325 name="category" | |
| 326 type="text" | |
| 327 value="Default" | |
| 328 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/> | |
|
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329 <repeat name="data_tracks" title="Annotation Track"> |
|
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330 <conditional name="data_format"> |
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331 <param type="select" label="Track Type" name="data_format_select"> |
| 3 | 332 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> |
|
1
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333 <option value="pileup">BAM Pileups</option> |
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334 <option value="blast">Blast XML</option> |
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335 <option value="wiggle">BigWig XY</option> |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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336 <option value="vcf">VCF SNPs</option> |
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337 <!--<option value="sparql">SPARQL</option>--> |
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1
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338 </param> |
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339 <when value="blast"> |
| 3 | 340 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> |
|
1
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341 |
| 3 | 342 <param label="Features used in Blast Search" |
| 343 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." | |
| 344 format="gff3" | |
| 345 name="blast_parent" | |
| 346 optional="true" | |
| 347 type="data"/> | |
|
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348 |
| 3 | 349 <param label="Minimum Gap Size" |
| 350 help="before a new match_part feature is created" | |
| 351 name="min_gap" | |
| 352 type="integer" | |
| 353 value="10" | |
| 354 min="2" /> | |
|
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355 <param label="Is this a protein blast search?" |
| 3 | 356 type="boolean" |
| 357 name="is_protein" | |
| 358 truevalue="true" | |
| 359 falsevalue="false" /> | |
| 360 | |
|
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361 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
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ad4b9d7eae6a
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362 |
| 3 | 363 <expand macro="track_styling" |
| 364 classname="feature" | |
| 365 label="description" | |
| 366 description="Hit_titles" | |
| 367 height="600px"/> | |
| 368 <expand macro="color_selection" | |
| 369 token_scaling_lin_select="false" | |
| 370 token_scaling_log_select="true" /> | |
|
8
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371 <expand macro="track_menu" /> |
|
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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372 <expand macro="track_display" /> |
|
1
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373 </when> |
|
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374 <when value="vcf"> |
| 3 | 375 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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376 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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377 </when> |
|
497c6bb3b717
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378 <when value="gene_calls"> |
| 3 | 379 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> |
|
8
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380 <conditional name="match_part"> |
| 3 | 381 <param label="This is match/match_part data" |
| 382 type="boolean" | |
| 383 name="match_part_select" | |
| 384 truevalue="true" | |
| 385 falsevalue="false" /> | |
| 386 <when value="true"> | |
| 387 <param label="Match Part Feature Type" | |
| 388 name="name" | |
| 389 type="text" | |
| 390 value="match" | |
| 391 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" | |
| 392 optional="False"/> | |
| 393 </when> | |
| 394 <when value="false" /> | |
| 395 </conditional> | |
|
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|
396 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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397 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
|
ad4b9d7eae6a
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|
398 |
|
10
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399 <conditional name="track_config"> |
|
1a6d882d340d
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400 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> |
|
1a6d882d340d
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401 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> |
|
1a6d882d340d
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402 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> |
|
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403 </param> |
|
1a6d882d340d
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404 <when value="JBrowse/View/Track/CanvasFeatures"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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405 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false"> |
|
1a6d882d340d
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406 <param label="Transcript type" |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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407 name="transcriptType" |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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408 type="text" |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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409 value="" |
|
1a6d882d340d
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410 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')" |
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1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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411 optional="True"/> |
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1a6d882d340d
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412 <param label="Subfeatures type" |
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1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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413 name="subParts" |
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1a6d882d340d
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414 type="text" |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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415 value="" |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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416 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')" |
|
1a6d882d340d
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417 optional="True"/> |
|
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418 <param label="Implied UTRs" |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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419 name="impliedUTRs" |
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1a6d882d340d
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420 type="boolean" |
|
1a6d882d340d
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421 checked="false" |
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422 truevalue="true" |
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1a6d882d340d
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423 falsevalue="false" |
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1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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424 help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/> |
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425 </section> |
|
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426 </when> |
|
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427 <when value="JBrowse/View/Track/HTMLFeatures"> |
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69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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428 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false"> |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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429 <param label="Transcript type" |
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69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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430 name="transcriptType" |
|
69c5e9c0add0
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431 type="text" |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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432 value="" |
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69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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433 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')" |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents:
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diff
changeset
|
434 optional="True"/> |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents:
12
diff
changeset
|
435 </section> |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents:
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diff
changeset
|
436 </when> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
437 </conditional> |
| 3 | 438 <expand macro="track_styling" /> |
| 439 <expand macro="color_selection" /> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
440 <expand macro="track_menu" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
441 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
442 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
443 <when value="pileup"> |
| 3 | 444 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
| 445 <param label="Autogenerate SNP Track" | |
| 446 help="Not recommended for deep coverage BAM files" | |
| 447 type="boolean" | |
| 448 name="auto_snp" | |
| 449 truevalue="true" | |
| 450 falsevalue="false" /> | |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
451 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
452 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
453 <when value="wiggle"> |
| 3 | 454 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
| 455 | |
| 456 <param label="Use XYPlot" | |
| 457 help="instead of continuous colored band" | |
| 458 type="boolean" | |
| 459 name="xyplot" | |
| 460 truevalue="JBrowse/View/Track/Wiggle/XYPlot" | |
| 461 falsevalue="JBrowse/View/Track/Wiggle/Density" /> | |
| 462 <param label="Show variance band" | |
| 463 help="Only for XYPlots" | |
| 464 type="boolean" | |
| 465 name="var_band" | |
| 466 truevalue="true" | |
| 467 falsevalue="false" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
468 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
469 <conditional name="scaling"> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
470 <param type="select" label="Track Scaling" name="scale_select"> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
471 <option value="auto_local">Autoscale (local)</option> |
| 3 | 472 <option value="auto_global" selected="true">Autoscale (global)</option> |
| 473 <option value="fixed">Specify Min/Max</option> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
474 </param> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
475 <when value="auto_local"></when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
476 <when value="auto_global"></when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
477 <when value="fixed"> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
478 <param label="Track minimum" name="minimum" |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
479 type="integer" value="0" /> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
480 <param label="Track maximum" name="maximum" |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
481 type="integer" value="100" /> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
482 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
483 </conditional> |
| 3 | 484 <expand macro="color_selection_minmax" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
485 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
486 </when> |
|
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
|
487 <!-- |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
488 <when value="sparql"> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
489 <param type="text" label="SPARQL Server URL" name="url" /> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
490 <param type="text" label="Track Label" name="key" value="SPARQL Genes" /> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
491 <param type="text" label="SPARQL Query" name="query" area="true" /> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
492 <expand macro="track_display" /> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
493 </when> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
494 --> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
495 </conditional> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
496 </repeat> |
| 3 | 497 </repeat> |
| 498 | |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
499 <expand macro="general_options" /> |
| 3 | 500 <param type="hidden" name="uglyTestingHack" value="" /> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
501 </inputs> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
changeset
|
502 <outputs> |
| 3 | 503 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
changeset
|
504 </outputs> |
| 3 | 505 <tests> |
| 506 <test> | |
| 507 <!-- gencode --> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
508 <param name="reference_genome|genome_type_select" value="history"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
509 <param name="reference_genome|genomes" value="merlin.fa"/> |
| 3 | 510 <param name="gencode" value="1" /> |
| 511 <param name="standalone" value="Data Directory" /> | |
| 512 <param name="uglyTestingHack" value="enabled" /> | |
| 513 <output name="output" file="gencode/test-1.xml" lines_diff="4" /> | |
| 514 </test> | |
| 515 <test> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
516 <param name="reference_genome|genome_type_select" value="history"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
517 <param name="reference_genome|genomes" value="merlin.fa"/> |
| 3 | 518 <param name="gencode" value="11" /> |
| 519 <param name="standalone" value="Data Directory" /> | |
| 520 <param name="uglyTestingHack" value="enabled" /> | |
| 521 <output name="output" file="gencode/test.xml" lines_diff="4"/> | |
| 522 </test> | |
| 523 <test> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
524 <param name="reference_genome|genome_type_select" value="history"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
525 <param name="reference_genome|genomes" value="merlin.fa"/> |
| 3 | 526 <param name="gencode" value="11" /> |
| 527 <param name="standalone" value="Data Directory" /> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
528 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
529 <param name="category" value="Auto Coloured" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
530 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
531 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
532 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
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533 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
534 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
535 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
536 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
537 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
538 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
539 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
540 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
541 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
542 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
543 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
544 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
545 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
546 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
547 </repeat> |
| 3 | 548 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
549 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
550 <param name="category" value="Ignore Scale" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
551 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
552 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
553 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
554 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
555 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
556 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
557 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
558 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
559 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
560 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
561 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
562 <param name="color_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
563 <param name="style_color" value="#ff00ff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
564 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
565 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
566 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
567 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
568 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
569 </repeat> |
| 3 | 570 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
571 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
572 <param name="category" value="Scaled Colour" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
573 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
574 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
575 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
576 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
577 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
578 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
579 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
580 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
581 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
582 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
583 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
584 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
585 <param name="scale_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
586 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
587 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
588 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
589 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
590 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
591 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
592 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
593 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
594 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
595 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
596 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
597 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
598 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
599 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
600 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
601 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
602 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
603 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
604 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
605 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
606 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
607 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
608 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
609 <param name="scale_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
610 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
611 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
612 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
613 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
614 <param name="color_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
615 <param name="style_color" value="#0000ff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
616 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
617 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
618 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
619 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
620 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
621 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
622 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
623 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
624 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
625 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
626 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
627 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
628 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
629 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
630 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
631 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
632 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
633 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
634 <param name="scale_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
635 <param name="minimum" value="0"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
636 <param name="maximum" value="1000"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
637 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
638 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
639 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
640 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
641 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
642 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
643 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
644 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
645 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
646 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
647 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
648 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
649 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
650 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
651 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
652 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
653 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
654 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
655 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
656 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
657 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
658 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
659 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
660 <param name="scale_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
661 <param name="minimum" value="0"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
662 <param name="maximum" value="1000"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
663 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
664 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
665 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
666 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
667 <param name="color_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
668 <param name="style_color" value="#ff0000"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
669 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
670 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
671 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
672 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
673 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
674 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
675 </repeat> |
| 3 | 676 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
677 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
678 <param name="category" value="Realistic" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
679 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
680 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
681 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
682 <param name="annotation" value="gff3/interpro.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
683 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
684 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
685 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
686 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
687 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
688 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
689 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
690 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
691 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
692 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
693 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
694 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
695 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
696 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
697 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
698 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
699 <param name="annotation" value="gff3/2.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
700 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
701 <param name="match_part_select" value="true"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
702 <param name="name" value="cDNA_match"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
703 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
704 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
705 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
706 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
707 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
708 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
709 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
710 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
711 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
712 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
713 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
714 </repeat> |
| 3 | 715 |
| 716 <param name="uglyTestingHack" value="enabled" /> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
717 <output name="output" file="gff3/test.xml" lines_diff="24" /> |
| 3 | 718 </test> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
719 <test> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
720 <param name="reference_genome|genome_type_select" value="history"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
721 <param name="reference_genome|genomes" value="merlin.fa"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
722 <param name="gencode" value="11" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
723 <param name="standalone" value="Data Directory" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
724 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
725 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
726 <param name="category" value="With menu or index" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
727 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
728 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
729 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
730 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
731 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
732 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
733 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
734 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
735 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
736 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
737 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
738 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
739 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
740 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
741 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
742 <section name="jbmenu"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
743 <repeat name="track_menu"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
744 <param name="menu_action" value="iframeDialog"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
745 <param name="menu_label" value="Some menu item"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
746 <param name="menu_title" value="Frame title"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
747 <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
748 <param name="menu_icon" value="dijitIconNewTask"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
749 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
750 <repeat name="track_menu"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
751 <param name="menu_action" value="newWindow"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
752 <param name="menu_label" value="Another menu item"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
753 <param name="menu_title" value="Frame title 2"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
754 <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
755 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
756 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
757 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
758 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
759 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
760 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
761 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
762 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
763 <param name="index" value="true"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
764 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
765 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
766 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
767 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
768 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
769 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
770 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
771 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
772 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
773 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
774 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
775 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
776 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
777 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
778 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
779 <param name="uglyTestingHack" value="enabled" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
780 <output name="output" file="menus/test.xml" lines_diff="6"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
781 </test> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
782 <test> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
783 <param name="reference_genome|genome_type_select" value="history"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
784 <param name="reference_genome|genomes" value="merlin.fa"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
785 <param name="gencode" value="11" /> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
786 <param name="standalone" value="Data Directory" /> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
787 |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
788 <repeat name="track_groups"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
789 <param name="category" value="With canvas config" /> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
790 <repeat name="data_tracks"> |
|
1a6d882d340d
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791 <conditional name="data_format"> |
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792 <param name="data_format_select" value="gene_calls"/> |
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793 <param name="annotation" value="gff3/1.gff"/> |
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794 <conditional name="match_part"> |
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795 <param name="match_part_select" value="false"/> |
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796 </conditional> |
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797 <conditional name="track_config"> |
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798 <section name="canvas_options"> |
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799 <param name="transcriptType" value="transcript"/> |
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800 <param name="subParts" value="exon"/> |
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801 <param name="impliedUTRs" value="true"/> |
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802 </section> |
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803 </conditional> |
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804 <section name="jbcolor_scale"> |
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805 <conditional name="color_score"> |
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806 <param name="color_score_select" value="none"/> |
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807 </conditional> |
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808 <conditional name="color"> |
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809 <param name="color_select" value="automatic"/> |
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810 </conditional> |
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811 </section> |
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812 </conditional> |
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813 </repeat> |
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814 </repeat> |
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815 |
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816 <param name="uglyTestingHack" value="enabled" /> |
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817 <output name="output" file="track_config/test.xml" lines_diff="6"/> |
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818 </test> |
| 3 | 819 </tests> |
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820 <help><![CDATA[ |
| 3 | 821 JBrowse-in-Galaxy |
| 822 ================= | |
| 823 | |
| 824 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible | |
| 825 alternative to Trackster. | |
| 826 | |
| 827 The JBrowse-in-Galaxy (JiG) tool was written to help build complex | |
| 828 JBrowse installations straight from Galaxy, taking advantage of the | |
| 829 latest Galaxy features such as dataset collections, sections, and colour | |
| 830 pickers. It allows you to build up a JBrowse instance without worrying | |
| 831 about how to run the command line tools to format your data, and which | |
| 832 options need to be supplied and where. Additionally it comes with many | |
| 833 javascript functions to handle colouring of features which would be | |
| 834 nearly impossible to write without the assistance of this tool. | |
| 835 | |
| 836 The JBrowse-in-Galaxy tool is maintained by `Eric | |
| 837 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you | |
| 838 encounter missing features or bugs. | |
| 839 | |
| 840 Options | |
| 841 ------- | |
| 842 | |
| 843 The first option you encounter is the **Fasta Sequence(s)**. This option | |
| 844 now accepts multiple fasta files, allowing you to build JBrowse | |
| 845 instances that contain data for multiple genomes or chrosomomes | |
| 846 (generally known as "landmark features" in gff3 terminology.) Up to 30 | |
| 847 will be shown from the dropdown selector within JBrowse, this is a known | |
| 848 issue. | |
| 849 | |
| 850 **Standalone Instances** are a somewhat in-development feature. | |
| 851 Currently Galaxy copies the entire JBrowse directory in order to have a | |
| 852 complete, downloadable file that contains a ready-to-go JBrowse | |
| 853 instance. This is obviously an anti-feature because users don't want a | |
| 854 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse | |
| 855 dataset in their history, and admins don't want useless copies of | |
| 856 JBrowse on disk. Unfortunately we have not come up with the perfect | |
| 857 solution just yet, but we're working on it! In the meantime, users have | |
| 858 been given the option to produce just the ``data/`` directory. For those | |
| 859 unfamiliar with JBrowse, the ``data/`` directory contains processed data | |
| 860 files, but no way to view them. This feature is additionally implemented | |
| 861 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration. | |
| 862 | |
| 863 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse, | |
| 864 which allows users to specify a non standard genetic code, and have | |
| 865 JBrowse highlight the correct start and stop codons. If you would like | |
| 866 to use a coding table not provided by this list, please let | |
| 867 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for | |
| 868 this. | |
| 869 | |
| 870 **Track Groups** represent a set of tracks in a single category. These | |
| 871 can be used to let your users understand relationships between large | |
| 872 groups of tracks. | |
| 873 | |
| 874 .. image:: sections.png | |
| 875 | |
| 876 Annotation Tracks | |
| 877 ----------------- | |
| 878 | |
| 879 Within Track Groups, you have one or more **Annotation Tracks**. Each | |
| 880 Annotation Track is a groups of datasets which have similar styling. | |
| 881 This allows you to rapidly build up JBrowse instances without having to | |
| 882 configure tracks individually. A massive improvement over previous | |
| 883 versions. For example, if you have five different GFF3 files from | |
| 884 various gene callers that you wish to display, you can take advantage of | |
| 885 this feature to style all of them similarly. | |
| 886 | |
| 887 There are a few different types of tracks supported, each with their own | |
| 888 set of options: | |
| 889 | |
| 890 GFF3/BED/GBK | |
| 891 ~~~~~~~~~~~~ | |
| 892 | |
| 893 These are your standard feature tracks. They usually highlight genes, | |
| 894 mRNAs and other features of interest along a genomic region. The | |
| 895 underlying tool and this help documentation focus primarily on GFF3 | |
| 896 data, and have not been tested extensively with other formats. Automatic | |
| 897 min/max detection will likely fail under BED and GBK datasets. | |
| 898 | |
| 899 The data may be of a subclass we call **match/match part** data. This | |
| 900 consists of top level ``match`` features, with a child ``match_part`` | |
| 901 feature, and is often used in displaying alignments. (See "Alignments" | |
| 902 section on the `GFF3 | |
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903 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more |
| 3 | 904 information). If the data is match/match part, you will need to specify |
| 905 the top level match feature name, as it can be one of a few different SO | |
| 906 terms, and JiG does not yet have the ability to understand SO terms. | |
| 907 | |
| 908 Next up is the **Styling Options** section, which lets you control a few | |
| 909 properties on how the track is styled. Most of these you will not need | |
| 910 to configure and can safely leave on defaults. Occasionally you will | |
| 911 want to change what information is shown in the end product. | |
| 912 | |
| 913 .. image:: styling.png | |
| 914 | |
| 915 In the above image you can see some black text, and some blue text. The | |
| 916 source of the black text is configured with the **style.label** option, | |
| 917 and the source of the blue text is configured with the | |
| 918 **style.description** option. | |
| 919 | |
| 920 Feature Score Scaling & Colouring Options | |
| 921 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 922 | |
| 923 First, you need to choose between ignoring the score attribute of GFF3 | |
| 924 files, or using it. If you choose to ignore it, all features will be | |
| 925 coloured with a solid colour. If you choose to use it, features will | |
| 926 have slightly different colours based on their scores. | |
| 927 | |
| 928 .. image:: opacity.png | |
| 929 | |
| 930 If you choose **Ignore score**, you may choose between automatically | |
| 931 choosing a colour, or manually specifying one. The automatically chosen | |
| 932 colours vary along a brewer palette and generally look quite nice with | |
| 933 no human intervention required. The manual colour choice is somewhat | |
| 934 self explanatory. Clicking on the small coloured square will bring up a | |
| 935 colour palette. | |
| 936 | |
| 937 If you choose **Base on score**, you're faced with a dizzying array of | |
| 938 options. First is the function to map the colour choices to colour | |
| 939 values. JiG comes with a few functions built in such as linear scaling, | |
| 940 logarithmic scaling, and blast scaling. | |
| 941 | |
| 942 The **linear scaling** method says "take these values, and they map | |
| 943 directly to a range of output values". **Logarithmic scaling** says | |
| 944 "please take the log of the score before mapping", and **Blast scaling** | |
| 945 is further specialised to handle blast data more nicely. These are | |
| 946 convenience functions to help transform the wide array of possible | |
| 947 values in the GFF3 score attribute to more meaningful numbers. If you | |
| 948 need more comprehensive score scaling, it is recommended that you | |
| 949 pre-process your GFF3 files somehow. | |
| 950 | |
| 951 Once you've selected a scaling method, you can choose to manually | |
| 952 specify the minimum and maximum expected values, or you can let JiG | |
| 953 determine them for you automatically. | |
| 954 | |
| 955 Finally, opacity is the only mapping we currently provide. Future | |
| 956 iterations will attempt to improve upon this and provide more colour | |
| 957 scales. The Opacity option maps the highest scoring features to full | |
| 958 opacity, and everything else to lower ones. | |
| 959 | |
| 960 BAM Pileups | |
| 961 ~~~~~~~~~~~ | |
| 962 | |
| 963 We support BAM files and can automatically generate SNP tracks based on | |
| 964 that bam data. | |
| 965 | |
| 966 .. image:: bam.png | |
| 967 | |
| 968 This is *strongly discouraged* for high coverage density datasets. | |
| 969 Unfortunately there are no other configuration options exposed for bam | |
| 970 files. If you find JBrowse options you wish to see exposed, please let | |
| 971 `me <mailto:esr+jig@tamu.edu>`__ know. | |
| 972 | |
| 973 BlastXML | |
| 974 ~~~~~~~~ | |
| 975 | |
| 976 .. image:: blast.png | |
| 977 | |
| 978 JiG now supports both blastn and blastp datasets. JiG internally uses a | |
| 979 blastXML to gapped GFF3 tool to convert your blastxml datasets into a | |
| 980 format amenable to visualization in JBrowse. This tool is also | |
| 981 available separately from the IUC on the toolshed. | |
| 982 | |
| 983 **Minimum Gap Size** reflects how long a gap must be before it becomes a | |
| 984 real gap in the processed gff3 file. In the picture above, various sizes | |
| 985 of gaps can be seen. If the minimum gap size was set much higher, say | |
| 986 100nt, many of the smaller gaps would disappear, and the features on | |
| 987 both sides would be merged into one, longer feature. This setting is | |
| 988 inversely proportional to runtime and output file size. *Do not set this | |
| 989 to a low value for large datasets*. By setting this number lower, you | |
| 990 will have extremely large outputs and extremely long runtimes. The | |
| 991 default was configured based off of the author's experience, but the | |
| 992 author only works on small viruses. It is *strongly* recommended that | |
| 993 you filter your blast results before display, e.g. picking out the top | |
| 994 10 hits or so. | |
| 995 | |
| 996 **Protein blast search** option merely informs underlying tools that | |
| 997 they should adjust feature locations by 3x. | |
| 998 | |
| 999 Styling Options | |
| 1000 ^^^^^^^^^^^^^^^ | |
| 1001 | |
| 1002 Please see the styling options for GFF3 datasets, they are identical. | |
| 1003 | |
| 1004 Feature Score Scaling & Coloring Options | |
| 1005 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 1006 | |
| 1007 Please see the score scaling and colouring options for GFF3 datasets, | |
| 1008 they are identical. Remember to set your score scaling to "blast" method | |
| 1009 if you do use it. | |
| 1010 | |
| 1011 Bigwig XY | |
| 1012 ~~~~~~~~~ | |
| 1013 | |
| 1014 .. image:: bigwig.png | |
| 1015 | |
| 1016 **XYPlot** | |
| 1017 | |
| 1018 BigWig tracks can be displayed as a "density" plot which is continuous | |
| 1019 line which varies in colour, or as an "XYplot." XYplots are preferable | |
| 1020 for users to visually identify specific features in a bigwig track, | |
| 1021 however density tracks are more visually compact. | |
| 1022 | |
| 1023 **Variance Band** is an option available to XYPlots, and can be seen in | |
| 1024 the third and fourth tracks in the above picture. This overlays a mean | |
| 1025 line, and 1 and 2 standard deviation areas. | |
| 1026 | |
| 1027 **Track Scaling** is different from colour scaling, instead it | |
| 1028 configures how the track behaves inside of JBrowse. **Autoscaling | |
| 1029 globally** means that JBrowse will determine the minimum and maximum for | |
| 1030 the track, and fix the bounds of the viewport to that. E.g. if your | |
| 1031 track ranges from 1-1000, and the region you're currently zoomed to only | |
| 1032 goes from 0-50, then the viewport range will still show 1-1000. This is | |
| 1033 good for global genomic context. However you may wish to consider | |
| 1034 **autoscaling locally** instead. In the example of a region which varies | |
| 1035 from 0-50, autoscaling locally would cause the individual track's | |
| 1036 viewport to re-adjust and show just the 0-50 region. If neither of these | |
| 1037 options are palatable, you may manually hardcode the minimum and | |
| 1038 maximums for the track to scale to. | |
| 1039 | |
| 1040 Colour Options | |
| 1041 ^^^^^^^^^^^^^^ | |
| 1042 | |
| 1043 BigWig tracks have two colours in JBrowse, a positive and a negative | |
| 1044 colour. | |
| 1045 | |
| 1046 As always you may manually choose a colour, or let JiG choose for you. | |
| 1047 | |
| 1048 One of the more interesting options is the **Bicolor pivot**. This | |
| 1049 option allows you to control the point at which JBrowse switches from | |
| 1050 the positive colour to the negative. In the above graphic, you can see | |
| 1051 this has been configured to "mean" for the first two (orange and blue) | |
| 1052 tracks. | |
| 1053 | |
| 1054 VCFs/SNPs | |
| 1055 ~~~~~~~~~ | |
| 1056 | |
| 1057 These tracks do not support any special configuration. | |
| 1058 | |
| 1059 Known Issues | |
| 1060 ------------ | |
| 1061 | |
| 1062 - More than 30 landmark features cannot be listed in the manual | |
| 1063 selector. | |
| 1064 - Non GFF3 likely has issue with automatically determined min/max | |
| 1065 scores. Manually specify minimum and maximum score attributes, or do | |
| 1066 not use varied colours based on scores to avoid this issue. | |
| 1067 | |
|
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1068 |
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1069 @ATTRIBUTION@ |
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1070 ]]></help> |
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1071 <expand macro="citations"/> |
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1072 </tool> |