jbrowse: jbrowse.xml annotate

annotate jbrowse.xml @ 8:ad4b9d7eae6a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9

author	iuc
date	Tue, 29 Nov 2016 10:55:30 -0500
parents	ecbdfc775b9a
children	1a6d882d340d

rev	line source
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@">
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	2 <description>genome browser</description>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	3 <macros>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	4 <import>macros.xml</import>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	5 </macros>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	6 <expand macro="requirements"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	7 <expand macro="stdio"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	8 <command><![CDATA[
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	9
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	10 #if $action.action_select == "create":
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	11 mkdir -p $output.files_path &&
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	12 #else:
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	13 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	14 #end if
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	15
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	16 ## Copy the XML file into the directory, mostly for debugging
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	17 ## but nice if users want to reproduce locally
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	18 cp $trackxml $output.files_path/galaxy.xml &&
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	19
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	20 ## Once that's done, we run the python script to handle the real work
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	21 python $__tool_directory__/jbrowse.py
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	22
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	23 --jbrowse \${JBROWSE_SOURCE_DIR}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	24 #if str($standalone) == "Complete":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	25 --standalone
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	26 #end if
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	27
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	28 --outdir $output.files_path
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	29 $trackxml &&
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	30
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	31 #if str($standalone) == "Complete":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	32 mv $output.files_path/index.html $output;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	33 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	34 mv $dummyIndex $output;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	35 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	36
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	37
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	38 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	39 #if str($uglyTestingHack) == "enabled":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	40 mv $trackxml $output
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	41 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	42 ]]></command>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	43 <configfiles>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	44 <configfile name="dummyIndex">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	45 <![CDATA[
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	46 <html>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	47 <head>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	48 </head>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	49 <body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	50 <h1>JBrowse Data Directory</h1>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	51 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	52 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	53 started shipping with the ability to produce just the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	54 "data" directory from a JBrowse instance, rather than a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	55 complete, standalone instance. This was intended to be used
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	56 with the in-development Apollo integration, but may have other
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	57 uses as well.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	58 </p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	59 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	60 <u>This is not usable on its own</u>. The output dataset may be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	61 used with Apollo, or may be passed through the "JBrowse -
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	62 Convert to Standalone" tool in Galaxy to "upgrade" to a full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	63 JBrowse instance.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	64 </p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	65 </body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	66 </html>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	67 ]]>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	68 </configfile>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	69 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	70 <root>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	71 <metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	72 <gencode>$gencode</gencode>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	73 <genomes>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	74 #if str($reference_genome.genome_type_select) == "indexed":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	75 <genome>${reference_genome.genomes.fields.path}</genome>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	76 #else
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	77 #for $genome in $reference_genome.genomes:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	78 <genome>$genome</genome>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	79 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	80 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	81 </genomes>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	82 <general>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	83 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	84 <trackPadding>${jbgen.trackPadding}</trackPadding>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	85
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	86 <shareLink>${jbgen.shareLink}</shareLink>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	87 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	88 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	89 <show_nav>${jbgen.show_nav}</show_nav>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	90 <show_overview>${jbgen.show_overview}</show_overview>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	91 <show_menu>${jbgen.show_menu}</show_menu>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	92 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	93 </general>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	94 </metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	95 <tracks>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	96 #for $tg in $track_groups:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	97 #for $track in $tg.data_tracks:
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	98 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	99 <files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	100 #for $dataset in $track.data_format.annotation:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	101 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	102 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	103 </files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	104
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	105 <options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	106 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	107 <style>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	108 <className>${track.data_format.jbstyle.style_classname}</className>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	109 <description>${track.data_format.jbstyle.style_description}</description>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	110 <label>${track.data_format.jbstyle.style_label}</label>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	111 <height>${track.data_format.jbstyle.style_height}</height>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	112 </style>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	113 <scaling>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	114 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	115 <method>ignore</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	116 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	117 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	118 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	119 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	120 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	121 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	122 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	123 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	124 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	125 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	126 <scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	127 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	128
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	129 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	130 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	131 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	132 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	133 </scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	134 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	135 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	136 ## auto_color
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	137 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	138 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	139 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	140 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	141 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	142 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	143 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	144 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	145 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	146 </scaling>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	147 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	148 #for $menu_item in $track.data_format.jbmenu.track_menu:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	149 <menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	150 <action>${menu_item.menu_action}</action>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	151 #if str($menu_item.menu_label) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	152 <label>${menu_item.menu_label}</label>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	153 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	154 #if str($menu_item.menu_title) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	155 <title>${menu_item.menu_title}</title>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	156 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	157 #if str($menu_item.menu_url) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	158 <url>${menu_item.menu_url.replace("&", "&").replace("\"", """)}</url>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	159 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	160 #if str($menu_item.menu_icon) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	161 <iconClass>${menu_item.menu_icon}</iconClass>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	162 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	163 </menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	164 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	165 </menus>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	166 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	167
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	168 #if str($track.data_format.data_format_select) == "wiggle":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	169 <wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	170 <type>${track.data_format.xyplot}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	171 <variance_band>${track.data_format.var_band}</variance_band>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	172 #if str($track.data_format.scaling.scale_select) == "auto_local":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	173 <autoscale>local</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	174 #else if str($track.data_format.scaling.scale_select) == "auto_global":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	175 <autoscale>global</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	176 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	177 <min>${track.data_format.scaling.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	178 <max>${track.data_format.scaling.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	179 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	180
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	181 ## Wiggle tracks need special color config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	182 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	183 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	184 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	185 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	186 <color_pos>__auto__</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	187 <color_neg>__auto__</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	188 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	189
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	190 ## Bicolor pivot config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	191 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	192 <bicolor_pivot>zero</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	193 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	194 <bicolor_pivot>mean</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	195 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	196 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	197 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	198 </wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	199 #else if str($track.data_format.data_format_select) == "pileup":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	200 <pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	201 <auto_snp>${track.data_format.auto_snp}</auto_snp>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	202 <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	203 #for $dataset in $track.data_format.annotation:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	204 <bam_index>${dataset.metadata.bam_index}</bam_index>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	205 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	206 </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	207 </pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	208 #else if str($track.data_format.data_format_select) == "blast":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	209 <blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	210 #if str($track.data_format.blast_parent) != "":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	211 <parent>${track.data_format.blast_parent}</parent>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	212 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	213 <protein>${track.data_format.is_protein}</protein>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	214 <min_gap>${track.data_format.min_gap}</min_gap>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	215 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	216 </blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	217 #else if str($track.data_format.data_format_select) == "gene_calls":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	218 <gff>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	219 <trackType>${track.data_format.track_class}</trackType>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	220 #if $track.data_format.match_part.match_part_select:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	221 <match>${track.data_format.match_part.name}</match>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	222 #end if
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	223 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	224 </gff>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	225 ## #else if str($track.data_format.data_format_select) == "sparql":
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	226 ## <sparql>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	227 ## <url>${track.data_format.url}</url>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	228 ## <label>${track.data_format.label}</label>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	229 ## <!-- This is going to be an absolutey nightmare -->
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	230 ## <query>${track.data_format.query}</query>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	231 ## </sparql>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	232 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	233 </options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	234 </track>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	235 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	236 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	237 </tracks>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	238 </root>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	239 ]]></configfile>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	240 </configfiles>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	241 <inputs>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	242 <conditional name="reference_genome">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	243 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	244 <option selected="True" value="indexed">Use a built-in genome</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	245 <option value="history">Use a genome from history</option>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	246 </param>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	247 <when value="indexed">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	248 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	249 help="If your genome of interest is not listed, contact the Galaxy team"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	250 label="Select a reference genome"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	251 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	252 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	253 >
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	254 <options from_data_table="all_fasta">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	255 <filter column="2" type="sort_by" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	256 <validator message="No genomes are available for the selected input dataset" type="no_options" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	257 </options>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	258 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	259 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	260 <when value="history">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	261 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	262 format="fasta"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	263 label="Select the reference genome"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	264 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	265 type="data"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	266 multiple="True" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	267 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	268 </conditional>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	269
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	270 <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"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	271
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	272
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	273 <param label="Genetic Code" name="gencode" type="select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	274 <option value="1">1. The Standard Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	275 <option value="2">2. The Vertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	276 <option value="3">3. The Yeast Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	277 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	278 <option value="5">5. The Invertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	279 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	280 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	281 <option value="10">10. The Euplotid Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	282 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	283 <option value="12">12. The Alternative Yeast Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	284 <option value="13">13. The Ascidian Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	285 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	286 <option value="16">16. Chlorophycean Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	287 <option value="21">21. Trematode Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	288 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	289 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	290 <option value="24">24. Pterobranchia Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	291 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	292 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	293
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	294 <conditional name="action">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	295 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	296 <option value="create">New JBrowse Instance</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	297 <option value="update">Update exising JBrowse Instance</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	298 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	299 <when value="create" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	300 <when value="update">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	301 <param label="Previous JBrowse Instance"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	302 name="update_jbrowse"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	303 type="data"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	304 format="html" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	305 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	306 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	307
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	308 <repeat name="track_groups" title="Track Group">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	309 <param label="Track Category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	310 name="category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	311 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	312 value="Default"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	313 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	314 <repeat name="data_tracks" title="Annotation Track">
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	315 <conditional name="data_format">
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	316 <param type="select" label="Track Type" name="data_format_select">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	317 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	318 <option value="pileup">BAM Pileups</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	319 <option value="blast">Blast XML</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	320 <option value="wiggle">BigWig XY</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	321 <option value="vcf">VCF SNPs</option>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	322 <!--<option value="sparql">SPARQL</option>-->
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	323 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	324 <when value="blast">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	325 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	326
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	327 <param label="Features used in Blast Search"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	328 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."
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	329 format="gff3"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	330 name="blast_parent"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	331 optional="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	332 type="data"/>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	333
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	334 <param label="Minimum Gap Size"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	335 help="before a new match_part feature is created"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	336 name="min_gap"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	337 type="integer"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	338 value="10"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	339 min="2" />
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	340 <param label="Is this a protein blast search?"
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	341 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	342 name="is_protein"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	343 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	344 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	345
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	346 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	347
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	348 <expand macro="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	349 classname="feature"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	350 label="description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	351 description="Hit_titles"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	352 height="600px"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	353 <expand macro="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	354 token_scaling_lin_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	355 token_scaling_log_select="true" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	356 <expand macro="track_menu" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	357 <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	358 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	359 <when value="vcf">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	360 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	361 <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	362 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	363 <when value="gene_calls">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	364 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	365 <conditional name="match_part">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	366 <param label="This is match/match_part data"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	367 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	368 name="match_part_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	369 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	370 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	371 <when value="true">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	372 <param label="Match Part Feature Type"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	373 name="name"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	374 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	375 value="match"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	376 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"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	377 optional="False"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	378 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	379 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	380 </conditional>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	381
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	382 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	383
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	384 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	385 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	386 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	387 </param>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	388 <expand macro="track_styling" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	389 <expand macro="color_selection" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	390 <expand macro="track_menu" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	391 <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	392 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	393 <when value="pileup">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	394 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	395 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	396 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	397 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	398 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	399 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	400 falsevalue="false" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	401 <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	402 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	403 <when value="wiggle">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	404 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	405
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	406 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	407 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	408 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	409 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	410 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	411 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	412 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	413 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	414 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	415 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	416 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	417 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	418
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	419 <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	420 <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	421 <option value="auto_local">Autoscale (local)</option>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	422 <option value="auto_global" selected="true">Autoscale (global)</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	423 <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	424 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	425 <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	426 <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	427 <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	428 <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	429 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	430 <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	431 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	432 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	433 </conditional>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	434 <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	435 <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	436 </when>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	437 <!--
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	438 <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	439 <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	440 <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	441 <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	442 <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	443 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	444 -->
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	445 </conditional>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	446 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	447 </repeat>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	448
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	449 <expand macro="general_options" />
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	450 <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	451 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	452 <outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	453 <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 parents: diff changeset	454 </outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	455 <tests>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	456 <test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	457 <!-- gencode -->
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	458 <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	459 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	460 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	461 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	462 <param name="uglyTestingHack" value="enabled" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	463 <output name="output" file="gencode/test-1.xml" lines_diff="4" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	464 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	465 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	466 <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	467 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	468 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	469 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	470 <param name="uglyTestingHack" value="enabled" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	471 <output name="output" file="gencode/test.xml" lines_diff="4"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	472 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	473 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	474 <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	475 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	476 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	477 <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	478 <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	479 <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	480 <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	481 <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	482 <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	483 <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	484 <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	485 <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	486 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	487 <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	488 <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	489 <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	490 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	491 <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	492 <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	493 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	494 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	495 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	496 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	497 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	498
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	499 <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	500 <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	501 <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	502 <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	503 <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	504 <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	505 <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	506 <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	507 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	508 <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	509 <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	510 <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	511 <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	512 <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	513 <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	514 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	515 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	516 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	517 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	518 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	519 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	520
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	521 <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	522 <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	523 <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	524 <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	525 <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	526 <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	527 <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	528 <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	529 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	530 <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	531 <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	532 <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	533 <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	534 <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	535 <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	536 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	537 <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	538 <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	539 <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	540 <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	541 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	542 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	543 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	544 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	545 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	546 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	547 <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	548 <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	549 <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	550 <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	551 <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	552 <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	553 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	554 <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	555 <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	556 <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	557 <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	558 <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	559 <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	560 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	561 <conditional name="color_scheme">
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="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	563 <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	564 <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	565 <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	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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	568 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	569 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	570 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	571 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	572 <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	573 <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	574 <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	575 <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	576 <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	577 <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	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 <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	580 <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	581 <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	582 <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	583 <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	584 <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	585 <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	586 <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	587 </conditional>
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="color_scheme">
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="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	590 <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	591 <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	592 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	593 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	594 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	595 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	596 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	597 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	598 <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	599 <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	600 <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	601 <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	602 <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	603 <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	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 <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	606 <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	607 <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	608 <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	609 <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	610 <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	611 <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	612 <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	613 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	614 <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	615 <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	616 <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	617 <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	618 <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	619 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	620 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	621 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	622 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	623 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	624 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	625 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	626
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	627 <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	628 <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	629 <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	630 <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	631 <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	632 <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	633 <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	634 <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	635 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	636 <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	637 <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	638 <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	639 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	640 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	641 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	642 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	643 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	644 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	645 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	646 <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	647 <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	648 <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	649 <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	650 <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	651 <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	652 <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	653 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	654 <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	655 <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	656 <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	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 name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	659 <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	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 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	662 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	663 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	664 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	665
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	666 <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	667 <output name="output" file="gff3/test.xml" lines_diff="24" />
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	668 </test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	669 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	670 <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	671 <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	672 <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	673 <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	674
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	675 <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	676 <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	677 <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	678 <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	679 <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	680 <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	681 <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	682 <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	683 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	684 <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	685 <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	686 <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	687 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	688 <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	689 <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	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>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	692 <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	693 <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	694 <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	695 <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	696 <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	697 <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	698 <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	699 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	700 <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	701 <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	702 <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	703 <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	704 <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	705 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	706 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	707 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	708 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	709 <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	710 <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	711 <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	712 <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	713 <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	714 <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	715 <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	716 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	717 <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	718 <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	719 <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	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 <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	722 <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	723 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	724 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	725 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	726 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	727 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	728
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	729 <param name="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	730 <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	731 </test>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	732 </tests>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	733 <help><![CDATA[
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	734 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	735 =================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	736
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	737 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	738 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	739
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	740 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	741 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	742 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	743 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	744 about how to run the command line tools to format your data, and which
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	745 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	746 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	747 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	748
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	749 The JBrowse-in-Galaxy tool is maintained by `Eric
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	750 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	751 encounter missing features or bugs.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	752
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	753 Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	754 -------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	755
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	756 The first option you encounter is the Fasta Sequence(s). This option
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	757 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	758 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	759 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	760 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	761 issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	762
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	763 Standalone Instances are a somewhat in-development feature.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	764 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	765 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	766 instance. This is obviously an anti-feature because users don't want a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	767 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	768 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	769 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	770 solution just yet, but we're working on it! In the meantime, users have
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	771 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	772 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	773 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	774 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	775
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	776 Genetic Code is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	777 which allows users to specify a non standard genetic code, and have
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	778 JBrowse highlight the correct start and stop codons. If you would like
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	779 to use a coding table not provided by this list, please let
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	780 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	781 this.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	782
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	783 Track Groups represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	784 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	785 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	786
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	787 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	788
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	789 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	790 -----------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	791
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	792 Within Track Groups, you have one or more Annotation Tracks. Each
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	793 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	794 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	795 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	796 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	797 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	798 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	799
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	800 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	801 set of options:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	802
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	803 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	804 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	805
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	806 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	807 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	808 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	809 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	810 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	811
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	812 The data may be of a subclass we call match/match part data. This
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	813 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	814 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	815 section on the `GFF3
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	816 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	817 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	818 the top level match feature name, as it can be one of a few different SO
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	819 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	820
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	821 Next up is the Styling Options section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	822 properties on how the track is styled. Most of these you will not need
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	823 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	824 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	825
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	826 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	827
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	828 In the above image you can see some black text, and some blue text. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	829 source of the black text is configured with the style.label option,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	830 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	831 style.description option.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	832
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	833 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	834 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	835
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	836 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	837 files, or using it. If you choose to ignore it, all features will be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	838 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	839 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	840
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	841 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	842
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	843 If you choose Ignore score, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	844 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	845 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	846 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	847 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	848 colour palette.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	849
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	850 If you choose Base on score, you're faced with a dizzying array of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	851 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	852 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	853 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	854
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	855 The linear scaling method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	856 directly to a range of output values". Logarithmic scaling says
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	857 "please take the log of the score before mapping", and Blast scaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	858 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	859 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	860 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	861 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	862 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	863
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	864 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	865 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	866 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	867
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	868 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	869 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	870 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	871 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	872
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	873 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	874 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	875
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	876 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	877 that bam data.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	878
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	879 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	880
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	881 This is strongly discouraged for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	882 Unfortunately there are no other configuration options exposed for bam
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	883 files. If you find JBrowse options you wish to see exposed, please let
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	884 `me <mailto:esr+jig@tamu.edu>`__ know.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	885
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	886 BlastXML
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	887 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	888
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	889 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	890
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	891 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	892 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	893 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	894 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	895
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	896 Minimum Gap Size reflects how long a gap must be before it becomes a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	897 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	898 of gaps can be seen. If the minimum gap size was set much higher, say
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	899 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	900 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	901 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	902 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	903 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	904 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	905 author only works on small viruses. It is strongly recommended that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	906 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	907 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	908
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	909 Protein blast search option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	910 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	911
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	912 Styling Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	913 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	914
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	915 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	916
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	917 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	918 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	919
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	920 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	921 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	922 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	923
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	924 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	925 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	926
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	927 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	928
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	929 XYPlot
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	930
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	931 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	932 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	933 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	934 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	935
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	936 Variance Band is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	937 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	938 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	939
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	940 Track Scaling is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	941 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	942 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	943 the track, and fix the bounds of the viewport to that. E.g. if your
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	944 track ranges from 1-1000, and the region you're currently zoomed to only
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	945 goes from 0-50, then the viewport range will still show 1-1000. This is
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	946 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	947 autoscaling locally instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	948 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	949 viewport to re-adjust and show just the 0-50 region. If neither of these
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	950 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	951 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	952
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	953 Colour Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	954 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	955
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	956 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	957 colour.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	958
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	959 As always you may manually choose a colour, or let JiG choose for you.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	960
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	961 One of the more interesting options is the Bicolor pivot. This
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	962 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	963 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	964 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	965 tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	966
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	967 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	968 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	969
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	970 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	971
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	972 Known Issues
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	973 ------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	974
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	975 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	976 selector.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	977 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	978 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	979 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	980
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	981
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	982 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	983 ]]></help>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	984 <expand macro="citations"/>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	985 </tool>

Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 8:ad4b9d7eae6a draft