jbrowse: jbrowse.xml annotate

annotate jbrowse.xml @ 17:ff11d442feed draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257

author	iuc
date	Wed, 15 Nov 2017 15:15:27 -0500
parents	b5c5470d7c09
children	836d1aa3e89a

rev	line source
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 13 diff changeset	1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.2">
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"/>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	8 <version_command>python jbrowse.py --version</version_command>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	9 <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	10
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	11 #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	12 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	13 #else:
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	14 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	15 #end if
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	16
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	17 ## Copy the XML file into the directory, mostly for debugging
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	18 ## but nice if users want to reproduce locally
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	19 cp $trackxml $output.files_path/galaxy.xml &&
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	20
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	21 ## 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	22 python $__tool_directory__/jbrowse.py
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	23
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	24 --jbrowse \${JBROWSE_SOURCE_DIR}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	25 #if str($standalone) == "Complete":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	26 --standalone
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	27 #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	28
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	29 --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	30 $trackxml &&
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	31
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	32 #if str($standalone) == "Complete":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	33 mv $output.files_path/index.html $output;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	34 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	35 mv $dummyIndex $output;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	36 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	37
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	38
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	39 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	40 #if str($uglyTestingHack) == "enabled":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	41 mv $trackxml $output
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	42 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	43 ]]></command>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	44 <configfiles>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	45 <configfile name="dummyIndex">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	46 <![CDATA[
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	47 <html>
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 </head>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	50 <body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	51 <h1>JBrowse Data Directory</h1>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	52 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	53 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	54 started shipping with the ability to produce just the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	55 "data" directory from a JBrowse instance, rather than a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	56 complete, standalone instance. This was intended to be used
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	57 with the in-development Apollo integration, but may have other
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	58 uses as well.
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 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	61 <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	62 used with Apollo, or may be passed through the "JBrowse -
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	63 Convert to Standalone" tool in Galaxy to "upgrade" to a full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	64 JBrowse instance.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	65 </p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	66 </body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	67 </html>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	68 ]]>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	69 </configfile>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	70 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	71 <root>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	72 <metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	73 <gencode>$gencode</gencode>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	74 <genomes>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	75 #if str($reference_genome.genome_type_select) == "indexed":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	76 <genome>${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	77 #else
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	78 #for $genome in $reference_genome.genomes:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	79 <genome path="$genome">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	80 <metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	81 <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	82 size="${genome.get_size(nice_size=True)}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	83 edam_format="${genome.datatype.edam_format}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	84 file_ext="${genome.ext}" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	85 <history id="${__app__.security.encode_id($genome.history_id)}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	86 user_email="${genome.history.user.email}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	87 user_id="${genome.history.user_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	88 display_name="${genome.history.get_display_name()}"/>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	89 <metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	90 #for (key, value) in $genome.get_metadata().items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	91 #if "_types" not in $key:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	92 ${key}="${value}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	93 #end if
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	94 #end for
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	95 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	96 <tool
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	97 tool_id="${genome.creating_job.tool_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	98 tool_version="${genome.creating_job.tool_version}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	99 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	100 </metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	101 </genome>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	102 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	103 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	104 </genomes>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	105 <general>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	106 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	107 <trackPadding>${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	108
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	109 <shareLink>${jbgen.shareLink}</shareLink>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	110 <aboutDescription>${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	111 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	112 <show_nav>${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	113 <show_overview>${jbgen.show_overview}</show_overview>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	114 <show_menu>${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	115 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	116 </general>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	117 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	118 </metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	119 <tracks>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	120 #for $tg in $track_groups:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	121 #for $track in $tg.data_tracks:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	122 #if $track.data_format.data_format_select == "rest":
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	123 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	124 <url>${track.data_format.url}</url>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	125 </track>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	126 #else:
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	127 <track cat="${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	128 <files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	129 #for $dataset in $track.data_format.annotation:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	130 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	131 <metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	132 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	133 size="${dataset.get_size(nice_size=True)}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	134 edam_format="${dataset.datatype.edam_format}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	135 file_ext="${dataset.ext}" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	136 <history id="${__app__.security.encode_id($dataset.history_id)}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	137 user_email="${dataset.history.user.email}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	138 user_id="${dataset.history.user_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	139 display_name="${dataset.history.get_display_name()}"/>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	140 <metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	141 #for (key, value) in $dataset.get_metadata().items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	142 #if "_types" not in $key:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	143 ${key}="${value}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	144 #end if
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	145 #end for
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	146 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	147 <tool
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	148 tool_id="${dataset.creating_job.tool_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	149 tool_version="${dataset.creating_job.tool_version}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	150 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	151 </metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	152 </trackFile>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	153 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	154 </files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	155
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	156 <options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	157 #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	158 <style>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	159 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	160 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	161 <className>${track.data_format.jbstyle.style_classname}</className>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	162 <description>${track.data_format.jbstyle.style_description}</description>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	163 <label>${track.data_format.jbstyle.style_label}</label>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	164 <height>${track.data_format.jbstyle.style_height}</height>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	165 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	166 </style>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	167 <scaling>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	168 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	169 <method>ignore</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	170 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	171 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	172 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	173 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	174 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	175 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	176 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	177 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	178 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	179 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	180 <scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	181 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	182
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	183 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	184 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	185 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	186 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	187 </scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	188 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	189 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	190 ## auto_color
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	191 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	192 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	193 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	194 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	195 <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	196 #end if
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 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	199 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	200 </scaling>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	201 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	202 #for $menu_item in $track.data_format.jbmenu.track_menu:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	203 <menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	204 <action>${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	205 #if str($menu_item.menu_label) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	206 <label>${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	207 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	208 #if str($menu_item.menu_title) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	209 <title>${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	210 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	211 #if str($menu_item.menu_url) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	212 <url>${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	213 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	214 #if str($menu_item.menu_icon) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	215 <iconClass>${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	216 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	217 </menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	218 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	219 </menus>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	220 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	221
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	222 #if str($track.data_format.data_format_select) == "wiggle":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	223 <wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	224 <type>${track.data_format.xyplot}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	225 <variance_band>${track.data_format.var_band}</variance_band>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	226 #if str($track.data_format.scaling.scale_select) == "auto_local":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	227 <autoscale>local</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	228 #else if str($track.data_format.scaling.scale_select) == "auto_global":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	229 <autoscale>global</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	230 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	231 <min>${track.data_format.scaling.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	232 <max>${track.data_format.scaling.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	233 #end if
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	234 <scale>${track.data_format.scale_select2}</scale>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	235
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	236 ## Wiggle tracks need special color config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	237 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	238 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	239 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	240 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	241 <color_pos>__auto__</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	242 <color_neg>__auto__</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	243 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	244
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	245 ## Bicolor pivot config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	246 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	247 <bicolor_pivot>zero</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	248 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	249 <bicolor_pivot>mean</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	250 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	251 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	252 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	253 </wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	254 #else if str($track.data_format.data_format_select) == "pileup":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	255 <pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	256 <auto_snp>${track.data_format.auto_snp}</auto_snp>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	257 <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	258 #for $dataset in $track.data_format.annotation:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	259 <bam_index>${dataset.metadata.bam_index}</bam_index>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	260 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	261 </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	262 </pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	263 #else if str($track.data_format.data_format_select) == "blast":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	264 <blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	265 #if str($track.data_format.blast_parent) != "":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	266 <parent>${track.data_format.blast_parent}</parent>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	267 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	268 <protein>${track.data_format.is_protein}</protein>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	269 <min_gap>${track.data_format.min_gap}</min_gap>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	270 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	271 </blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	272 #else if str($track.data_format.data_format_select) == "gene_calls":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	273 <gff>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	274 <trackType>${track.data_format.track_config.track_class}</trackType>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	275 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	276 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	277 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	278 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	279 #if str($track.data_format.track_config.canvas_options.subParts) != "":
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	280 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	281 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	282 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	283 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	284 #end if
13 69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	285 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures':
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	286 #if str($track.data_format.track_config.html_options.transcriptType) != "":
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	287 <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType>
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	288 #end if
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	289 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	290 #if $track.data_format.match_part.match_part_select:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	291 <match>${track.data_format.match_part.name}</match>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	292 #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	293 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	294 </gff>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	295 ## #else if str($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	296 ## <sparql>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	297 ## <url>${track.data_format.url}</url>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	298 ## <label>${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	299 ## <!-- 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	300 ## <query>${track.data_format.query}</query>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	301 ## </sparql>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	302 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	303 </options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	304 </track>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	305 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	306 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	307 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	308 </tracks>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	309 <plugins
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	310 ComboTrackSelector="${plugins.ComboTrackSelector}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	311 Bookmarks="${plugins.Bookmarks}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	312 GCContent="${plugins.GCContent}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	313 theme="${plugins.theme}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	314 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	315 </root>]]></configfile>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	316 </configfiles>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	317 <inputs>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	318 <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	319 <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	320 <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	321 <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	322 </param>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	323 <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	324 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	325 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	326 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	327 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	328 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	329 >
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	330 <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	331 <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	332 <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	333 </options>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	334 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	335 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	336 <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	337 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	338 format="fasta"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	339 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	340 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	341 type="data"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	342 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	343 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	344 </conditional>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	345
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	346 <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	347
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	348 <param label="Genetic Code" name="gencode" type="select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	349 <option value="1">1. The Standard Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	350 <option value="2">2. The Vertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	351 <option value="3">3. The Yeast Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	352 <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	353 <option value="5">5. The Invertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	354 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	355 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	356 <option value="10">10. The Euplotid Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	357 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	358 <option value="12">12. The Alternative Yeast Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	359 <option value="13">13. The Ascidian Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	360 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	361 <option value="16">16. Chlorophycean Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	362 <option value="21">21. Trematode Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	363 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	364 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	365 <option value="24">24. Pterobranchia Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	366 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	367 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	368
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	369 <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	370 <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	371 <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	372 <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	373 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	374 <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	375 <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	376 <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	377 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	378 type="data"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	379 format="html" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	380 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	381 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	382
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	383 <repeat name="track_groups" title="Track Group">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	384 <param label="Track Category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	385 name="category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	386 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	387 value="Default"
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	388 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	389 <repeat name="data_tracks" title="Annotation Track">
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	390 <conditional name="data_format" label="Track Options">
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	391 <param type="select" label="Track Type" name="data_format_select">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	392 <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	393 <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	394 <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	395 <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	396 <option value="vcf">VCF SNPs</option>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	397 <option value="rest">REST Endpoint</option>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	398 <!--<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	399 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	400 <when value="blast">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	401 <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	402
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	403 <param label="Features used in Blast Search"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	404 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	405 format="gff3"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	406 name="blast_parent"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	407 optional="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	408 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	409
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	410 <param label="Minimum Gap Size"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	411 help="before a new match_part feature is created"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	412 name="min_gap"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	413 type="integer"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	414 value="10"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	415 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	416 <param label="Is this a protein blast search?"
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	417 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	418 name="is_protein"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	419 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	420 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	421
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	422 <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	423
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	424 <expand macro="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	425 classname="feature"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	426 label="description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	427 description="Hit_titles"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	428 height="600px"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	429 <expand macro="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	430 token_scaling_lin_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	431 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	432 <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	433 <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	434 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	435 <when value="vcf">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	436 <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	437 <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	438 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	439 <when value="gene_calls">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	440 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	441 <conditional name="match_part" label="match/match_part data">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	442 <param label="This is match/match_part data"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	443 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	444 name="match_part_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	445 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	446 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	447 <when value="true">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	448 <param label="Match Part Feature Type"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	449 name="name"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	450 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	451 value="match"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	452 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	453 optional="False"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	454 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	455 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	456 </conditional>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	457
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	458 <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	459
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	460 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	461 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	462 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	463 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	464 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	465 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	466 <when value="JBrowse/View/Track/CanvasFeatures">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	467 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	468 <param label="Transcript type"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	469 name="transcriptType"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	470 type="text"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	471 value=""
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	472 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	473 optional="True"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	474 <param label="Subfeatures type"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	475 name="subParts"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	476 type="text"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	477 value=""
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	478 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	479 optional="True"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	480 <param label="Implied UTRs"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	481 name="impliedUTRs"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	482 type="boolean"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	483 checked="false"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	484 truevalue="true"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	485 falsevalue="false"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	486 help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	487 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	488 </when>
13 69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	489 <when value="JBrowse/View/Track/HTMLFeatures">
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	490 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false">
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	491 <param label="Transcript type"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	492 name="transcriptType"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	493 type="text"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	494 value=""
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	495 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	496 optional="True"/>
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	497 </section>
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	498 </when>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	499 </conditional>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	500 <expand macro="track_styling" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	501 <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	502 <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	503 <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	504 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	505 <when value="pileup">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	506 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	507 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	508 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	509 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	510 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	511 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	512 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	513 <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	514 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	515 <when value="wiggle">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	516 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	517
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	518 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	519 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	520 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	521 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	522 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	523 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	524 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	525 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	526 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	527 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	528 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	529 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	530
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	531 <conditional name="scaling" label="Scaling">
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	532 <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	533 <option value="auto_local">Autoscale (local)</option>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	534 <option value="auto_global" selected="true">Autoscale (global)</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	535 <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	536 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	537 <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	538 <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	539 <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	540 <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	541 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	542 <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	543 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	544 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	545 </conditional>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	546 <param type="select" label="Visual Scaling" name="scale_select2">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	547 <option value="linear" selected="true">Linear</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	548 <option value="log">Logarithmic (Dynamically Calculated)</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	549 </param>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	550 <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	551 <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	552 </when>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	553 <when value="rest">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	554 <param type="text" label="REST Endpoint" name="url" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	555 </when>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	556 <!--
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	557 <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	558 <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	559 <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	560 <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	561 <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	562 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	563 -->
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	564 </conditional>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	565 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	566 </repeat>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	567
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	568 <expand macro="general_options" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	569 <section name="plugins" title="Plugins" expanded="false">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	570 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	571 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	572 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	573 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	574 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	575 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	576
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	577 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	578 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	579 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	580
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	581 <param type="select" label="JBrowse Theme" name="theme">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	582 <option value="" selected="True">Default</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	583 <option value="Minimalist">Minimalist</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	584 <option value="Dark">Dark</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	585 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	586 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	587
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	588 <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	589 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	590 <outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	591 <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	592 </outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	593 <tests>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	594 <test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	595 <!-- gencode -->
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	596 <param name="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	597 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	598 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	599 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	600 <param name="uglyTestingHack" value="enabled" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	601 <output name="output" file="gencode/test-1.xml" lines_diff="4" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	602 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	603 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	604 <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	605 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	606 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	607 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	608 <param name="uglyTestingHack" value="enabled" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	609 <output name="output" file="gencode/test.xml" lines_diff="14"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	610 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	611 <test>
8 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="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	613 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	614 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	615 <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	616 <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	617 <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	618 <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	619 <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	620 <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	621 <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	622 <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	623 <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	624 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	625 <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	626 <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	627 <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	628 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	629 <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	630 <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	631 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	632 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	633 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	634 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	635 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	636
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	637 <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	638 <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	639 <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	640 <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	641 <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	642 <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	643 <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	644 <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	645 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	646 <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	647 <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	648 <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	649 <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	650 <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	651 <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	652 </conditional>
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>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	655 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	656 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	657 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	658
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	659 <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	660 <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	661 <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	662 <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	663 <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	664 <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	665 <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	666 <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	667 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	668 <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	669 <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	670 <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	671 <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	672 <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	673 <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	674 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	675 <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	676 <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	677 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	678 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	679 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	680 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	681 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	682 </section>
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 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	685 <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	686 <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	687 <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	688 <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	689 <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	690 <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	691 </conditional>
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="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	693 <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	694 <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	695 <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	696 <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	697 <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	698 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	699 <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	700 <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	701 <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	702 <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	703 <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	704 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	705 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	706 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	707 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	708 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	709 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	710 <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	711 <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	712 <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	713 <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	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="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	720 <param name="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	721 <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	722 <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	723 <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	724 <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	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 <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	727 <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	728 <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	729 <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	730 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	731 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	732 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	733 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	734 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	735 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	736 <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	737 <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	738 <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	739 <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	740 <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	741 <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	742 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	743 <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	744 <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	745 <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	746 <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	747 <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	748 <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	749 <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	750 <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	751 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	752 <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	753 <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	754 <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	755 <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	756 <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	757 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	758 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	759 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	760 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	761 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	762 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	763 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	764
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	765 <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	766 <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	767 <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	768 <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	769 <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	770 <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	771 <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	772 <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	773 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	774 <section 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	775 <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	776 <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	777 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	778 <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	779 <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	780 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	781 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	782 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	783 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	784 <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	785 <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	786 <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	787 <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	788 <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	789 <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	790 <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	791 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	792 <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	793 <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	794 <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	795 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	796 <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	797 <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	798 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	799 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	800 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	801 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	802 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	803
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	804 <param name="uglyTestingHack" value="enabled" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	805 <output name="output" file="gff3/test.xml" lines_diff="64" />
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	806 </test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	807 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	808 <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	809 <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	810 <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	811 <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	812
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	813 <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	814 <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	815 <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	816 <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	817 <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	818 <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	819 <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	820 <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	821 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	822 <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	823 <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	824 <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	825 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	826 <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	827 <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	828 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	829 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	830 <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	831 <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	832 <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	833 <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	834 <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	835 <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	836 <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	837 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	838 <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	839 <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	840 <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	841 <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	842 <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	843 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	844 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	845 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	846 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	847 <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	848 <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	849 <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	850 <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	851 <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	852 <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	853 <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	854 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	855 <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	856 <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	857 <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	858 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	859 <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	860 <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	861 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	862 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	863 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	864 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	865 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	866
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	867 <param name="uglyTestingHack" value="enabled" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	868 <output name="output" file="menus/test.xml" lines_diff="24"/>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	869 </test>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	870 <test>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	871 <param name="reference_genome\|genome_type_select" value="history"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	872 <param name="reference_genome\|genomes" value="merlin.fa"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	873 <param name="gencode" value="11" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	874 <param name="standalone" value="Data Directory" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	875
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	876 <repeat name="track_groups">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	877 <param name="category" value="With canvas config" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	878 <repeat name="data_tracks">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	879 <conditional name="data_format">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	880 <param name="data_format_select" value="gene_calls"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	881 <param name="annotation" value="gff3/1.gff"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	882 <conditional name="match_part">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	883 <param name="match_part_select" value="false"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	884 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	885 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	886 <section name="canvas_options">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	887 <param name="transcriptType" value="transcript"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	888 <param name="subParts" value="exon"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	889 <param name="impliedUTRs" value="true"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	890 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	891 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	892 <section name="jbcolor_scale">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	893 <conditional name="color_score">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	894 <param name="color_score_select" value="none"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	895 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	896 <conditional name="color">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	897 <param name="color_select" value="automatic"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	898 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	899 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	900 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	901 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	902 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	903
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	904 <param name="uglyTestingHack" value="enabled" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	905 <output name="output" file="track_config/test.xml" lines_diff="26"/>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	906 </test>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	907 </tests>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	908 <help><![CDATA[
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	909 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	910 =================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	911
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	912 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	913 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	914
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	915 Overview
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	916 --------
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	917
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	918 JBrowse is a fast, embeddable genome browser built completely with
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	919 JavaScript and HTML5.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	920
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	921 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	922 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	923 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	924 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	925 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	926 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	927 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	928 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	929
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	930 The JBrowse-in-Galaxy tool is maintained by `Eric
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	931 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	932 encounter missing features or bugs.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	933
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	934 Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	935 -------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	936
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	937 The first option you encounter is the Fasta Sequence(s). This option
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	938 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	939 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	940 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	941 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	942 issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	943
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	944 Standalone Instances are a somewhat in-development feature.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	945 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	946 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	947 instance. This is obviously an anti-feature because users don't want a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	948 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	949 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	950 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	951 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	952 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	953 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	954 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	955 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	956
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	957 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	958 which allows users to specify a non standard genetic code, and have
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	959 JBrowse highlight the correct start and stop codons. If you would like
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	960 to use a coding table not provided by this list, please let
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	961 `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	962 this.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	963
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	964 Track Groups represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	965 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	966 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	967
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	968 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	969
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	970 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	971 -----------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	972
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	973 Within Track Groups, you have one or more Annotation Tracks. Each
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	974 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	975 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	976 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	977 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	978 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	979 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	980
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	981 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	982 set of options:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	983
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	984 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	985 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	986
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	987 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	988 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	989 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	990 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	991 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	992
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	993 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	994 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	995 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	996 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	997 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	998 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	999 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	1000 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1001
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1002 Next up is the Styling Options section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1003 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	1004 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1005 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1006
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1007 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1008
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1009 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	1010 source of the black text is configured with the style.label option,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1011 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1012 style.description option.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1013
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1014 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1015 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1016
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1017 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1018 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	1019 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1020 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1021
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1022 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1023
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1024 If you choose Ignore score, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1025 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1026 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1027 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1028 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1029 colour palette.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1030
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1031 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	1032 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1033 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1034 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1035
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1036 The linear scaling method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1037 directly to a range of output values". Logarithmic scaling says
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1038 "please take the log of the score before mapping", and Blast scaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1039 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1040 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1041 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1042 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1043 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1044
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1045 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1046 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1047 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1048
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1049 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1050 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1051 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1052 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1053
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1054 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1055 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1056
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1057 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1058 that bam data.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1059
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1060 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1061
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1062 This is strongly discouraged for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1063 Unfortunately there are no other configuration options exposed for bam
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1064 files. If you find JBrowse options you wish to see exposed, please let
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1065 `me <mailto:esr+jig@tamu.edu>`__ know.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1066
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1067 BlastXML
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1068 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1069
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1070 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1071
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1072 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1073 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1074 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1075 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1076
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1077 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	1078 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1079 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	1080 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1081 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1082 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1083 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1084 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1085 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1086 author only works on small viruses. It is strongly recommended that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1087 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1088 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1089
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1090 Protein blast search option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1091 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1092
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1093 Styling Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1094 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1095
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1096 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1097
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1098 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1099 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1100
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1101 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1102 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1103 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1104
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1105 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1106 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1107
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1108 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1109
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1110 XYPlot
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1111
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1112 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1113 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1114 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1115 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1116
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1117 Variance Band is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1118 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1119 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1120
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1121 Track Scaling is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1122 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1123 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1124 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	1125 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	1126 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	1127 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1128 autoscaling locally instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1129 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1130 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	1131 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1132 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1133
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1134 Colour Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1135 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1136
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1137 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1138 colour.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1139
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1140 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	1141
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1142 One of the more interesting options is the Bicolor pivot. This
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1143 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1144 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1145 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1146 tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1147
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1148 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1149 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1150
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1151 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1152
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1153 Known Issues
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1154 ------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1155
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1156 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1157 selector.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1158 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1159 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1160 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1161
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1162
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1163 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1164 ]]></help>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	1165 <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	1166 </tool>

Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 17:ff11d442feed draft