Mercurial > repos > iuc > jbrowse
annotate jbrowse.xml @ 11:4cbceec1d6b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 172014e3f03ea00dfd5fcd689e1246d001e82288
| author | iuc |
|---|---|
| date | Wed, 14 Dec 2016 09:19:48 -0500 |
| parents | 1a6d882d340d |
| children | db5fe5a3176a |
| rev | line source |
|---|---|
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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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6
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changeset
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1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@"> |
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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
parents:
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:
diff
changeset
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5 </macros> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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:
diff
changeset
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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
parents:
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changeset
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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
parents:
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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
parents:
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changeset
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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
parents:
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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
parents:
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changeset
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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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changeset
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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 $__tool_directory__/jbrowse.py | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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22 |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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23 --jbrowse \${JBROWSE_SOURCE_DIR} |
| 3 | 24 #if str($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
parents:
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changeset
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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
parents:
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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
parents:
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changeset
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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 $output | |
| 41 #end if | |
| 42 ]]></command> | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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43 <configfiles> |
| 3 | 44 <configfile name="dummyIndex"> |
| 45 <![CDATA[ | |
| 46 <html> | |
| 47 <head> | |
| 48 </head> | |
| 49 <body> | |
| 50 <h1>JBrowse Data Directory</h1> | |
| 51 <p> | |
| 52 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?) | |
| 53 started shipping with the ability to produce just the | |
| 54 "data" directory from a JBrowse instance, rather than a | |
| 55 complete, standalone instance. This was intended to be used | |
| 56 with the in-development Apollo integration, but may have other | |
| 57 uses as well. | |
| 58 </p> | |
| 59 <p> | |
| 60 <u>This is not usable on its own</u>. The output dataset may be | |
| 61 used with Apollo, or may be passed through the "JBrowse - | |
| 62 Convert to Standalone" tool in Galaxy to "upgrade" to a full | |
| 63 JBrowse instance. | |
| 64 </p> | |
| 65 </body> | |
| 66 </html> | |
| 67 ]]> | |
| 68 </configfile> | |
| 69 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> | |
| 70 <root> | |
| 71 <metadata> | |
| 72 <gencode>$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:
6
diff
changeset
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74 #if str($reference_genome.genome_type_select) == "indexed": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
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75 <genome>${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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diff
changeset
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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:
6
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changeset
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77 #for $genome in $reference_genome.genomes: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
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78 <genome>$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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diff
changeset
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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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changeset
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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
parents:
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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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diff
changeset
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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
parents:
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changeset
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86 <shareLink>${jbgen.shareLink}</shareLink> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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changeset
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87 <aboutDescription>${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
parents:
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diff
changeset
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88 <show_tracklist>${jbgen.show_tracklist}</show_tracklist> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
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89 <show_nav>${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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diff
changeset
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90 <show_overview>${jbgen.show_overview}</show_overview> |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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changeset
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91 <show_menu>${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
parents:
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changeset
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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
parents:
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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
iuc
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148 #for $menu_item in $track.data_format.jbmenu.track_menu: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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149 <menu> |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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150 <action>${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
iuc
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151 #if str($menu_item.menu_label) != "": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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152 <label>${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($menu_item.menu_title) != "": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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155 <title>${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
iuc
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157 #if str($menu_item.menu_url) != "": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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158 <url>${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
parents:
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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 #end if |
| 3 | 231 #if $track.data_format.match_part.match_part_select: |
| 232 <match>${track.data_format.match_part.name}</match> | |
| 233 #end if | |
|
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234 <index>${track.data_format.index}</index> |
| 3 | 235 </gff> |
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236 ## #else if str($track.data_format.data_format_select) == "sparql": |
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237 ## <sparql> |
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238 ## <url>${track.data_format.url}</url> |
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239 ## <label>${track.data_format.label}</label> |
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240 ## <!-- This is going to be an absolutey nightmare --> |
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241 ## <query>${track.data_format.query}</query> |
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242 ## </sparql> |
| 3 | 243 #end if |
| 244 </options> | |
| 245 </track> | |
| 246 #end for | |
| 247 #end for | |
| 248 </tracks> | |
| 249 </root> | |
|
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250 ]]></configfile> |
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251 </configfiles> |
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252 <inputs> |
|
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253 <conditional name="reference_genome"> |
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254 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> |
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255 <option selected="True" value="indexed">Use a built-in genome</option> |
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256 <option value="history">Use a genome from history</option> |
|
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257 </param> |
|
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258 <when value="indexed"> |
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259 <param |
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260 help="If your genome of interest is not listed, contact the Galaxy team" |
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261 label="Select a reference genome" |
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262 name="genomes" |
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263 type="select" |
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264 > |
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265 <options from_data_table="all_fasta"> |
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266 <filter column="2" type="sort_by" /> |
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267 <validator message="No genomes are available for the selected input dataset" type="no_options" /> |
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268 </options> |
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269 </param> |
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270 </when> |
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271 <when value="history"> |
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272 <param |
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273 format="fasta" |
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274 label="Select the reference genome" |
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275 name="genomes" |
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276 type="data" |
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277 multiple="True" /> |
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278 </when> |
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279 </conditional> |
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280 |
| 3 | 281 <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"/> |
| 282 | |
|
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283 |
| 3 | 284 <param label="Genetic Code" name="gencode" type="select"> |
| 285 <option value="1">1. The Standard Code</option> | |
| 286 <option value="2">2. The Vertebrate Mitochondrial Code</option> | |
| 287 <option value="3">3. The Yeast Mitochondrial Code</option> | |
| 288 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
| 289 <option value="5">5. The Invertebrate Mitochondrial Code</option> | |
| 290 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
| 291 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option> | |
| 292 <option value="10">10. The Euplotid Nuclear Code</option> | |
| 293 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option> | |
| 294 <option value="12">12. The Alternative Yeast Nuclear Code</option> | |
| 295 <option value="13">13. The Ascidian Mitochondrial Code</option> | |
| 296 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option> | |
| 297 <option value="16">16. Chlorophycean Mitochondrial Code</option> | |
| 298 <option value="21">21. Trematode Mitochondrial Code</option> | |
| 299 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option> | |
| 300 <option value="23">23. Thraustochytrium Mitochondrial Code</option> | |
| 301 <option value="24">24. Pterobranchia Mitochondrial Code</option> | |
| 302 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> | |
| 303 </param> | |
| 304 | |
|
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305 <conditional name="action"> |
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306 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> |
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307 <option value="create">New JBrowse Instance</option> |
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308 <option value="update">Update exising JBrowse Instance</option> |
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309 </param> |
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310 <when value="create" /> |
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311 <when value="update"> |
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312 <param label="Previous JBrowse Instance" |
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313 name="update_jbrowse" |
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314 type="data" |
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315 format="html" /> |
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316 </when> |
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317 </conditional> |
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318 |
| 3 | 319 <repeat name="track_groups" title="Track Group"> |
| 320 <param label="Track Category" | |
| 321 name="category" | |
| 322 type="text" | |
| 323 value="Default" | |
| 324 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/> | |
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325 <repeat name="data_tracks" title="Annotation Track"> |
|
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326 <conditional name="data_format"> |
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327 <param type="select" label="Track Type" name="data_format_select"> |
| 3 | 328 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> |
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329 <option value="pileup">BAM Pileups</option> |
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330 <option value="blast">Blast XML</option> |
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497c6bb3b717
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331 <option value="wiggle">BigWig XY</option> |
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332 <option value="vcf">VCF SNPs</option> |
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333 <!--<option value="sparql">SPARQL</option>--> |
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334 </param> |
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335 <when value="blast"> |
| 3 | 336 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> |
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337 |
| 3 | 338 <param label="Features used in Blast Search" |
| 339 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." | |
| 340 format="gff3" | |
| 341 name="blast_parent" | |
| 342 optional="true" | |
| 343 type="data"/> | |
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344 |
| 3 | 345 <param label="Minimum Gap Size" |
| 346 help="before a new match_part feature is created" | |
| 347 name="min_gap" | |
| 348 type="integer" | |
| 349 value="10" | |
| 350 min="2" /> | |
|
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351 <param label="Is this a protein blast search?" |
| 3 | 352 type="boolean" |
| 353 name="is_protein" | |
| 354 truevalue="true" | |
| 355 falsevalue="false" /> | |
| 356 | |
|
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357 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
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ad4b9d7eae6a
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358 |
| 3 | 359 <expand macro="track_styling" |
| 360 classname="feature" | |
| 361 label="description" | |
| 362 description="Hit_titles" | |
| 363 height="600px"/> | |
| 364 <expand macro="color_selection" | |
| 365 token_scaling_lin_select="false" | |
| 366 token_scaling_log_select="true" /> | |
|
8
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367 <expand macro="track_menu" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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368 <expand macro="track_display" /> |
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1
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369 </when> |
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370 <when value="vcf"> |
| 3 | 371 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> |
|
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372 <expand macro="track_display" /> |
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1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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373 </when> |
|
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374 <when value="gene_calls"> |
| 3 | 375 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> |
|
8
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376 <conditional name="match_part"> |
| 3 | 377 <param label="This is match/match_part data" |
| 378 type="boolean" | |
| 379 name="match_part_select" | |
| 380 truevalue="true" | |
| 381 falsevalue="false" /> | |
| 382 <when value="true"> | |
| 383 <param label="Match Part Feature Type" | |
| 384 name="name" | |
| 385 type="text" | |
| 386 value="match" | |
| 387 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" | |
| 388 optional="False"/> | |
| 389 </when> | |
| 390 <when value="false" /> | |
| 391 </conditional> | |
|
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392 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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393 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
|
ad4b9d7eae6a
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394 |
|
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395 <conditional name="track_config"> |
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396 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> |
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397 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> |
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398 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> |
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399 </param> |
|
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400 <when value="JBrowse/View/Track/CanvasFeatures"> |
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401 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false"> |
|
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402 <param label="Transcript type" |
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403 name="transcriptType" |
|
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404 type="text" |
|
1a6d882d340d
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405 value="" |
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406 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')" |
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407 optional="True"/> |
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408 <param label="Subfeatures type" |
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409 name="subParts" |
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410 type="text" |
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1a6d882d340d
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411 value="" |
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412 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')" |
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413 optional="True"/> |
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414 <param label="Implied UTRs" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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415 name="impliedUTRs" |
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416 type="boolean" |
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417 checked="false" |
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418 truevalue="true" |
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419 falsevalue="false" |
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420 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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421 </section> |
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422 </when> |
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423 <when value="JBrowse/View/Track/HTMLFeatures" /> |
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424 </conditional> |
| 3 | 425 <expand macro="track_styling" /> |
| 426 <expand macro="color_selection" /> | |
|
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427 <expand macro="track_menu" /> |
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428 <expand macro="track_display" /> |
|
1
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429 </when> |
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430 <when value="pileup"> |
| 3 | 431 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
| 432 <param label="Autogenerate SNP Track" | |
| 433 help="Not recommended for deep coverage BAM files" | |
| 434 type="boolean" | |
| 435 name="auto_snp" | |
| 436 truevalue="true" | |
| 437 falsevalue="false" /> | |
|
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438 <expand macro="track_display" /> |
|
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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439 </when> |
|
497c6bb3b717
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440 <when value="wiggle"> |
| 3 | 441 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
| 442 | |
| 443 <param label="Use XYPlot" | |
| 444 help="instead of continuous colored band" | |
| 445 type="boolean" | |
| 446 name="xyplot" | |
| 447 truevalue="JBrowse/View/Track/Wiggle/XYPlot" | |
| 448 falsevalue="JBrowse/View/Track/Wiggle/Density" /> | |
| 449 <param label="Show variance band" | |
| 450 help="Only for XYPlots" | |
| 451 type="boolean" | |
| 452 name="var_band" | |
| 453 truevalue="true" | |
| 454 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
|
455 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
456 <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
|
457 <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:
0
diff
changeset
|
458 <option value="auto_local">Autoscale (local)</option> |
| 3 | 459 <option value="auto_global" selected="true">Autoscale (global)</option> |
| 460 <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
|
461 </param> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
462 <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
|
463 <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
|
464 <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
|
465 <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
|
466 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
|
467 <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
|
468 type="integer" value="100" /> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
469 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
470 </conditional> |
| 3 | 471 <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
|
472 <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
|
473 </when> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
474 <!-- |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
475 <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
|
476 <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
|
477 <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
|
478 <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
|
479 <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
|
480 </when> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
481 --> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
482 </conditional> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
483 </repeat> |
| 3 | 484 </repeat> |
| 485 | |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
486 <expand macro="general_options" /> |
| 3 | 487 <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
|
488 </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
|
489 <outputs> |
| 3 | 490 <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
|
491 </outputs> |
| 3 | 492 <tests> |
| 493 <test> | |
| 494 <!-- gencode --> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
495 <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
|
496 <param name="reference_genome|genomes" value="merlin.fa"/> |
| 3 | 497 <param name="gencode" value="1" /> |
| 498 <param name="standalone" value="Data Directory" /> | |
| 499 <param name="uglyTestingHack" value="enabled" /> | |
| 500 <output name="output" file="gencode/test-1.xml" lines_diff="4" /> | |
| 501 </test> | |
| 502 <test> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
503 <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
|
504 <param name="reference_genome|genomes" value="merlin.fa"/> |
| 3 | 505 <param name="gencode" value="11" /> |
| 506 <param name="standalone" value="Data Directory" /> | |
| 507 <param name="uglyTestingHack" value="enabled" /> | |
| 508 <output name="output" file="gencode/test.xml" lines_diff="4"/> | |
| 509 </test> | |
| 510 <test> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
511 <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
|
512 <param name="reference_genome|genomes" value="merlin.fa"/> |
| 3 | 513 <param name="gencode" value="11" /> |
| 514 <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
|
515 <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
|
516 <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
|
517 <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
|
518 <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
|
519 <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
|
520 <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
|
521 <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
|
522 <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
|
523 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
524 <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
|
525 <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
|
526 <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
|
527 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
528 <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
|
529 <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
|
530 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
531 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
532 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
533 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
534 </repeat> |
| 3 | 535 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
536 <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
|
537 <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
|
538 <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
|
539 <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
|
540 <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
|
541 <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
|
542 <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
|
543 <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
|
544 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
545 <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
|
546 <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
|
547 <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
|
548 <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
|
549 <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
|
550 <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
|
551 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
552 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
553 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
554 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
555 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
556 </repeat> |
| 3 | 557 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
558 <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
|
559 <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
|
560 <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
|
561 <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
|
562 <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
|
563 <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
|
564 <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
|
565 <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
|
566 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
567 <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
|
568 <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
|
569 <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
|
570 <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
|
571 <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
|
572 <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
|
573 </conditional> |
|
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="color_scheme"> |
|
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="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
|
576 <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
|
577 <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
|
578 </conditional> |
|
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 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
581 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
582 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
583 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
584 <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
|
585 <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
|
586 <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
|
587 <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
|
588 <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
|
589 <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
|
590 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
591 <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
|
592 <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
|
593 <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
|
594 <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
|
595 <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
|
596 <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
|
597 </conditional> |
|
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="color_scheme"> |
|
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="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
|
600 <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
|
601 <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
|
602 <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
|
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 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
605 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
606 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
607 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
608 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
609 <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
|
610 <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
|
611 <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
|
612 <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
|
613 <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
|
614 <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
|
615 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
616 <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
|
617 <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
|
618 <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
|
619 <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
|
620 <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
|
621 <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
|
622 <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
|
623 <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
|
624 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
625 <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
|
626 <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
|
627 <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
|
628 <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
|
629 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
630 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
631 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
632 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
633 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
634 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
635 <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
|
636 <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
|
637 <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
|
638 <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
|
639 <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
|
640 <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
|
641 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
642 <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
|
643 <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
|
644 <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
|
645 <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
|
646 <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
|
647 <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
|
648 <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
|
649 <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
|
650 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
651 <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
|
652 <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
|
653 <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
|
654 <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
|
655 <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
|
656 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
657 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
658 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
659 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
660 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
661 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
662 </repeat> |
| 3 | 663 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
664 <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
|
665 <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
|
666 <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
|
667 <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
|
668 <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
|
669 <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
|
670 <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
|
671 <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
|
672 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
673 <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
|
674 <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
|
675 <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
|
676 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
677 <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
|
678 <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
|
679 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
680 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
681 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
682 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
683 <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
|
684 <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
|
685 <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
|
686 <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
|
687 <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
|
688 <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
|
689 <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
|
690 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
691 <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
|
692 <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
|
693 <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
|
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 <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
|
696 <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
|
697 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
698 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
699 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
700 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
701 </repeat> |
| 3 | 702 |
| 703 <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
|
704 <output name="output" file="gff3/test.xml" lines_diff="24" /> |
| 3 | 705 </test> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
706 <test> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
707 <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
|
708 <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
|
709 <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
|
710 <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
|
711 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
712 <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
|
713 <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
|
714 <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
|
715 <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
|
716 <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
|
717 <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
|
718 <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
|
719 <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
|
720 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
721 <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
|
722 <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
|
723 <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
|
724 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
725 <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
|
726 <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
|
727 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
728 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
729 <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
|
730 <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
|
731 <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
|
732 <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
|
733 <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
|
734 <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
|
735 <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
|
736 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
737 <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
|
738 <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
|
739 <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
|
740 <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
|
741 <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
|
742 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
743 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
744 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
745 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
746 <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
|
747 <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
|
748 <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
|
749 <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
|
750 <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
|
751 <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
|
752 <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
|
753 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
754 <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
|
755 <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
|
756 <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
|
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 <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
|
759 <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
|
760 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
761 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
762 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
763 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
764 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
765 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
766 <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
|
767 <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
|
768 </test> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
769 <test> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
770 <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
|
771 <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
|
772 <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
|
773 <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
|
774 |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
775 <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
|
776 <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
|
777 <repeat name="data_tracks"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
778 <conditional name="data_format"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
779 <param name="data_format_select" value="gene_calls"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
780 <param name="annotation" value="gff3/1.gff"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
781 <conditional name="match_part"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
782 <param name="match_part_select" value="false"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
783 </conditional> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
784 <conditional name="track_config"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
785 <section name="canvas_options"> |
|
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="transcriptType" value="transcript"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
787 <param name="subParts" value="exon"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
788 <param name="impliedUTRs" value="true"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
789 </section> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
790 </conditional> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
791 <section name="jbcolor_scale"> |
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1a6d882d340d
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792 <conditional name="color_score"> |
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793 <param name="color_score_select" value="none"/> |
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794 </conditional> |
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795 <conditional name="color"> |
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796 <param name="color_select" value="automatic"/> |
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797 </conditional> |
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798 </section> |
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799 </conditional> |
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800 </repeat> |
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801 </repeat> |
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802 |
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803 <param name="uglyTestingHack" value="enabled" /> |
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804 <output name="output" file="track_config/test.xml" lines_diff="6"/> |
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805 </test> |
| 3 | 806 </tests> |
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807 <help><![CDATA[ |
| 3 | 808 JBrowse-in-Galaxy |
| 809 ================= | |
| 810 | |
| 811 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible | |
| 812 alternative to Trackster. | |
| 813 | |
| 814 The JBrowse-in-Galaxy (JiG) tool was written to help build complex | |
| 815 JBrowse installations straight from Galaxy, taking advantage of the | |
| 816 latest Galaxy features such as dataset collections, sections, and colour | |
| 817 pickers. It allows you to build up a JBrowse instance without worrying | |
| 818 about how to run the command line tools to format your data, and which | |
| 819 options need to be supplied and where. Additionally it comes with many | |
| 820 javascript functions to handle colouring of features which would be | |
| 821 nearly impossible to write without the assistance of this tool. | |
| 822 | |
| 823 The JBrowse-in-Galaxy tool is maintained by `Eric | |
| 824 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you | |
| 825 encounter missing features or bugs. | |
| 826 | |
| 827 Options | |
| 828 ------- | |
| 829 | |
| 830 The first option you encounter is the **Fasta Sequence(s)**. This option | |
| 831 now accepts multiple fasta files, allowing you to build JBrowse | |
| 832 instances that contain data for multiple genomes or chrosomomes | |
| 833 (generally known as "landmark features" in gff3 terminology.) Up to 30 | |
| 834 will be shown from the dropdown selector within JBrowse, this is a known | |
| 835 issue. | |
| 836 | |
| 837 **Standalone Instances** are a somewhat in-development feature. | |
| 838 Currently Galaxy copies the entire JBrowse directory in order to have a | |
| 839 complete, downloadable file that contains a ready-to-go JBrowse | |
| 840 instance. This is obviously an anti-feature because users don't want a | |
| 841 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse | |
| 842 dataset in their history, and admins don't want useless copies of | |
| 843 JBrowse on disk. Unfortunately we have not come up with the perfect | |
| 844 solution just yet, but we're working on it! In the meantime, users have | |
| 845 been given the option to produce just the ``data/`` directory. For those | |
| 846 unfamiliar with JBrowse, the ``data/`` directory contains processed data | |
| 847 files, but no way to view them. This feature is additionally implemented | |
| 848 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration. | |
| 849 | |
| 850 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse, | |
| 851 which allows users to specify a non standard genetic code, and have | |
| 852 JBrowse highlight the correct start and stop codons. If you would like | |
| 853 to use a coding table not provided by this list, please let | |
| 854 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for | |
| 855 this. | |
| 856 | |
| 857 **Track Groups** represent a set of tracks in a single category. These | |
| 858 can be used to let your users understand relationships between large | |
| 859 groups of tracks. | |
| 860 | |
| 861 .. image:: sections.png | |
| 862 | |
| 863 Annotation Tracks | |
| 864 ----------------- | |
| 865 | |
| 866 Within Track Groups, you have one or more **Annotation Tracks**. Each | |
| 867 Annotation Track is a groups of datasets which have similar styling. | |
| 868 This allows you to rapidly build up JBrowse instances without having to | |
| 869 configure tracks individually. A massive improvement over previous | |
| 870 versions. For example, if you have five different GFF3 files from | |
| 871 various gene callers that you wish to display, you can take advantage of | |
| 872 this feature to style all of them similarly. | |
| 873 | |
| 874 There are a few different types of tracks supported, each with their own | |
| 875 set of options: | |
| 876 | |
| 877 GFF3/BED/GBK | |
| 878 ~~~~~~~~~~~~ | |
| 879 | |
| 880 These are your standard feature tracks. They usually highlight genes, | |
| 881 mRNAs and other features of interest along a genomic region. The | |
| 882 underlying tool and this help documentation focus primarily on GFF3 | |
| 883 data, and have not been tested extensively with other formats. Automatic | |
| 884 min/max detection will likely fail under BED and GBK datasets. | |
| 885 | |
| 886 The data may be of a subclass we call **match/match part** data. This | |
| 887 consists of top level ``match`` features, with a child ``match_part`` | |
| 888 feature, and is often used in displaying alignments. (See "Alignments" | |
| 889 section on the `GFF3 | |
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890 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more |
| 3 | 891 information). If the data is match/match part, you will need to specify |
| 892 the top level match feature name, as it can be one of a few different SO | |
| 893 terms, and JiG does not yet have the ability to understand SO terms. | |
| 894 | |
| 895 Next up is the **Styling Options** section, which lets you control a few | |
| 896 properties on how the track is styled. Most of these you will not need | |
| 897 to configure and can safely leave on defaults. Occasionally you will | |
| 898 want to change what information is shown in the end product. | |
| 899 | |
| 900 .. image:: styling.png | |
| 901 | |
| 902 In the above image you can see some black text, and some blue text. The | |
| 903 source of the black text is configured with the **style.label** option, | |
| 904 and the source of the blue text is configured with the | |
| 905 **style.description** option. | |
| 906 | |
| 907 Feature Score Scaling & Colouring Options | |
| 908 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 909 | |
| 910 First, you need to choose between ignoring the score attribute of GFF3 | |
| 911 files, or using it. If you choose to ignore it, all features will be | |
| 912 coloured with a solid colour. If you choose to use it, features will | |
| 913 have slightly different colours based on their scores. | |
| 914 | |
| 915 .. image:: opacity.png | |
| 916 | |
| 917 If you choose **Ignore score**, you may choose between automatically | |
| 918 choosing a colour, or manually specifying one. The automatically chosen | |
| 919 colours vary along a brewer palette and generally look quite nice with | |
| 920 no human intervention required. The manual colour choice is somewhat | |
| 921 self explanatory. Clicking on the small coloured square will bring up a | |
| 922 colour palette. | |
| 923 | |
| 924 If you choose **Base on score**, you're faced with a dizzying array of | |
| 925 options. First is the function to map the colour choices to colour | |
| 926 values. JiG comes with a few functions built in such as linear scaling, | |
| 927 logarithmic scaling, and blast scaling. | |
| 928 | |
| 929 The **linear scaling** method says "take these values, and they map | |
| 930 directly to a range of output values". **Logarithmic scaling** says | |
| 931 "please take the log of the score before mapping", and **Blast scaling** | |
| 932 is further specialised to handle blast data more nicely. These are | |
| 933 convenience functions to help transform the wide array of possible | |
| 934 values in the GFF3 score attribute to more meaningful numbers. If you | |
| 935 need more comprehensive score scaling, it is recommended that you | |
| 936 pre-process your GFF3 files somehow. | |
| 937 | |
| 938 Once you've selected a scaling method, you can choose to manually | |
| 939 specify the minimum and maximum expected values, or you can let JiG | |
| 940 determine them for you automatically. | |
| 941 | |
| 942 Finally, opacity is the only mapping we currently provide. Future | |
| 943 iterations will attempt to improve upon this and provide more colour | |
| 944 scales. The Opacity option maps the highest scoring features to full | |
| 945 opacity, and everything else to lower ones. | |
| 946 | |
| 947 BAM Pileups | |
| 948 ~~~~~~~~~~~ | |
| 949 | |
| 950 We support BAM files and can automatically generate SNP tracks based on | |
| 951 that bam data. | |
| 952 | |
| 953 .. image:: bam.png | |
| 954 | |
| 955 This is *strongly discouraged* for high coverage density datasets. | |
| 956 Unfortunately there are no other configuration options exposed for bam | |
| 957 files. If you find JBrowse options you wish to see exposed, please let | |
| 958 `me <mailto:esr+jig@tamu.edu>`__ know. | |
| 959 | |
| 960 BlastXML | |
| 961 ~~~~~~~~ | |
| 962 | |
| 963 .. image:: blast.png | |
| 964 | |
| 965 JiG now supports both blastn and blastp datasets. JiG internally uses a | |
| 966 blastXML to gapped GFF3 tool to convert your blastxml datasets into a | |
| 967 format amenable to visualization in JBrowse. This tool is also | |
| 968 available separately from the IUC on the toolshed. | |
| 969 | |
| 970 **Minimum Gap Size** reflects how long a gap must be before it becomes a | |
| 971 real gap in the processed gff3 file. In the picture above, various sizes | |
| 972 of gaps can be seen. If the minimum gap size was set much higher, say | |
| 973 100nt, many of the smaller gaps would disappear, and the features on | |
| 974 both sides would be merged into one, longer feature. This setting is | |
| 975 inversely proportional to runtime and output file size. *Do not set this | |
| 976 to a low value for large datasets*. By setting this number lower, you | |
| 977 will have extremely large outputs and extremely long runtimes. The | |
| 978 default was configured based off of the author's experience, but the | |
| 979 author only works on small viruses. It is *strongly* recommended that | |
| 980 you filter your blast results before display, e.g. picking out the top | |
| 981 10 hits or so. | |
| 982 | |
| 983 **Protein blast search** option merely informs underlying tools that | |
| 984 they should adjust feature locations by 3x. | |
| 985 | |
| 986 Styling Options | |
| 987 ^^^^^^^^^^^^^^^ | |
| 988 | |
| 989 Please see the styling options for GFF3 datasets, they are identical. | |
| 990 | |
| 991 Feature Score Scaling & Coloring Options | |
| 992 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 993 | |
| 994 Please see the score scaling and colouring options for GFF3 datasets, | |
| 995 they are identical. Remember to set your score scaling to "blast" method | |
| 996 if you do use it. | |
| 997 | |
| 998 Bigwig XY | |
| 999 ~~~~~~~~~ | |
| 1000 | |
| 1001 .. image:: bigwig.png | |
| 1002 | |
| 1003 **XYPlot** | |
| 1004 | |
| 1005 BigWig tracks can be displayed as a "density" plot which is continuous | |
| 1006 line which varies in colour, or as an "XYplot." XYplots are preferable | |
| 1007 for users to visually identify specific features in a bigwig track, | |
| 1008 however density tracks are more visually compact. | |
| 1009 | |
| 1010 **Variance Band** is an option available to XYPlots, and can be seen in | |
| 1011 the third and fourth tracks in the above picture. This overlays a mean | |
| 1012 line, and 1 and 2 standard deviation areas. | |
| 1013 | |
| 1014 **Track Scaling** is different from colour scaling, instead it | |
| 1015 configures how the track behaves inside of JBrowse. **Autoscaling | |
| 1016 globally** means that JBrowse will determine the minimum and maximum for | |
| 1017 the track, and fix the bounds of the viewport to that. E.g. if your | |
| 1018 track ranges from 1-1000, and the region you're currently zoomed to only | |
| 1019 goes from 0-50, then the viewport range will still show 1-1000. This is | |
| 1020 good for global genomic context. However you may wish to consider | |
| 1021 **autoscaling locally** instead. In the example of a region which varies | |
| 1022 from 0-50, autoscaling locally would cause the individual track's | |
| 1023 viewport to re-adjust and show just the 0-50 region. If neither of these | |
| 1024 options are palatable, you may manually hardcode the minimum and | |
| 1025 maximums for the track to scale to. | |
| 1026 | |
| 1027 Colour Options | |
| 1028 ^^^^^^^^^^^^^^ | |
| 1029 | |
| 1030 BigWig tracks have two colours in JBrowse, a positive and a negative | |
| 1031 colour. | |
| 1032 | |
| 1033 As always you may manually choose a colour, or let JiG choose for you. | |
| 1034 | |
| 1035 One of the more interesting options is the **Bicolor pivot**. This | |
| 1036 option allows you to control the point at which JBrowse switches from | |
| 1037 the positive colour to the negative. In the above graphic, you can see | |
| 1038 this has been configured to "mean" for the first two (orange and blue) | |
| 1039 tracks. | |
| 1040 | |
| 1041 VCFs/SNPs | |
| 1042 ~~~~~~~~~ | |
| 1043 | |
| 1044 These tracks do not support any special configuration. | |
| 1045 | |
| 1046 Known Issues | |
| 1047 ------------ | |
| 1048 | |
| 1049 - More than 30 landmark features cannot be listed in the manual | |
| 1050 selector. | |
| 1051 - Non GFF3 likely has issue with automatically determined min/max | |
| 1052 scores. Manually specify minimum and maximum score attributes, or do | |
| 1053 not use varied colours based on scores to avoid this issue. | |
| 1054 | |
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1055 |
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1056 @ATTRIBUTION@ |
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1057 ]]></help> |
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1058 <expand macro="citations"/> |
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1059 </tool> |