jbrowse: jbrowse.xml annotate

annotate jbrowse.xml @ 18:836d1aa3e89a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e

author	iuc
date	Thu, 16 Nov 2017 09:44:45 -0500
parents	ff11d442feed
children	8f33c9fbc119

rev	line source
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3">
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"/>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	8 <version_command>python '${__tool_directory__}/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 $output.files_path/galaxy.xml &&
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	20
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	21 ## Once that's done, we run the python script to handle the real work
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	22 python '$__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($reference_genome.genome_type_select) == "indexed":
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	76 <genome path="${reference_genome.genomes.fields.path}">
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	77 <metadata />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	78 </genome>s
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	79 #else
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	80 #for $genome in $reference_genome.genomes:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	81 <genome path="$genome">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	82 <metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	83 <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	84 size="${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	85 edam_format="${genome.datatype.edam_format}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	86 file_ext="${genome.ext}" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	87 <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	88 user_email="${genome.history.user.email}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	89 user_id="${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	90 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	91 <metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	92 #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	93 #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	94 ${key}="${value}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	95 #end if
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	96 #end for
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	97 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	98 <tool
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	99 tool_id="${genome.creating_job.tool_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	100 tool_version="${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	101 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	102 </metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	103 </genome>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	104 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	105 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	106 </genomes>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	107 <general>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	108 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	109 <trackPadding>${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	110
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	111 <shareLink>${jbgen.shareLink}</shareLink>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	112 <aboutDescription>${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	113 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	114 <show_nav>${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	115 <show_overview>${jbgen.show_overview}</show_overview>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	116 <show_menu>${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	117 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	118 </general>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	119 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	120 </metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	121 <tracks>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	122 #for $tg in $track_groups:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	123 #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	124 #if $track.data_format.data_format_select == "rest":
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	125 <track cat="${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	126 <url>${track.data_format.url}</url>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	127 </track>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	128 #else:
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	129 <track cat="${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	130 <files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	131 #for $dataset in $track.data_format.annotation:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	132 <trackFile path="${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	133 <metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	134 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	135 size="${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	136 edam_format="${dataset.datatype.edam_format}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	137 file_ext="${dataset.ext}" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	138 <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	139 user_email="${dataset.history.user.email}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	140 user_id="${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	141 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	142 <metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	143 #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	144 #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	145 ${key}="${value}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	146 #end if
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	147 #end for
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	148 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	149 <tool
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	150 tool_id="${dataset.creating_job.tool_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	151 tool_version="${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	152 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	153 </metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	154 </trackFile>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	155 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	156 </files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	157
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	158 <options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	159 #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	160 <style>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	161 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	162 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	163 <className>${track.data_format.jbstyle.style_classname}</className>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	164 <description>${track.data_format.jbstyle.style_description}</description>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	165 <label>${track.data_format.jbstyle.style_label}</label>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	166 <height>${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	167 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	168 </style>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	169 <scaling>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	170 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	171 <method>ignore</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	172 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	173 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	174 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	175 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	176 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	177 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	178 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	179 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	180 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	181 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	182 <scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	183 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	184
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	185 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	186 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	187 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	188 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	189 </scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	190 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	191 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	192 ## auto_color
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	193 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	194 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	195 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	196 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	197 <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	198 #end if
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 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	201 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	202 </scaling>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	203 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	204 #for $menu_item in $track.data_format.jbmenu.track_menu:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	205 <menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	206 <action>${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	207 #if str($menu_item.menu_label) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	208 <label>${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	209 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	210 #if str($menu_item.menu_title) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	211 <title>${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	212 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	213 #if str($menu_item.menu_url) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	214 <url>${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	215 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	216 #if str($menu_item.menu_icon) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	217 <iconClass>${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	218 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	219 </menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	220 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	221 </menus>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	222 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	223
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	224 #if str($track.data_format.data_format_select) == "wiggle":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	225 <wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	226 <type>${track.data_format.xyplot}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	227 <variance_band>${track.data_format.var_band}</variance_band>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	228 #if str($track.data_format.scaling.scale_select) == "auto_local":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	229 <autoscale>local</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	230 #else if str($track.data_format.scaling.scale_select) == "auto_global":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	231 <autoscale>global</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	232 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	233 <min>${track.data_format.scaling.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	234 <max>${track.data_format.scaling.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	235 #end if
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	236 <scale>${track.data_format.scale_select2}</scale>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	237
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	238 ## Wiggle tracks need special color config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	239 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	240 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	241 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	242 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	243 <color_pos>__auto__</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	244 <color_neg>__auto__</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	245 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	246
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	247 ## Bicolor pivot config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	248 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	249 <bicolor_pivot>zero</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	250 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	251 <bicolor_pivot>mean</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	252 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	253 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	254 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	255 </wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	256 #else if str($track.data_format.data_format_select) == "pileup":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	257 <pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	258 <auto_snp>${track.data_format.auto_snp}</auto_snp>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	259 <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	260 #for $dataset in $track.data_format.annotation:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	261 <bam_index>${dataset.metadata.bam_index}</bam_index>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	262 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	263 </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	264 </pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	265 #else if str($track.data_format.data_format_select) == "blast":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	266 <blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	267 #if str($track.data_format.blast_parent) != "":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	268 <parent>${track.data_format.blast_parent}</parent>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	269 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	270 <protein>${track.data_format.is_protein}</protein>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	271 <min_gap>${track.data_format.min_gap}</min_gap>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	272 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	273 </blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	274 #else if str($track.data_format.data_format_select) == "gene_calls":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	275 <gff>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	276 <trackType>${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	277 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	278 #if str($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	279 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	280 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	281 #if str($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	282 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	283 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	284 #if str($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	285 <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	286 #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	287 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures':
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	288 #if str($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	289 <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	290 #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	291 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	292 #if $track.data_format.match_part.match_part_select:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	293 <match>${track.data_format.match_part.name}</match>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	294 #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	295 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	296 </gff>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	297 ## #else if str($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	298 ## <sparql>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	299 ## <url>${track.data_format.url}</url>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	300 ## <label>${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	301 ## <!-- 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	302 ## <query>${track.data_format.query}</query>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	303 ## </sparql>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	304 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	305 </options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	306 </track>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	307 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	308 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	309 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	310 </tracks>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	311 <plugins
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	312 ComboTrackSelector="${plugins.ComboTrackSelector}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	313 Bookmarks="${plugins.Bookmarks}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	314 GCContent="${plugins.GCContent}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	315 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	316 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	317 </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	318 </configfiles>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	319 <inputs>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	320 <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	321 <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	322 <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	323 <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	324 </param>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	325 <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	326 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	327 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	328 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	329 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	330 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	331 >
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	332 <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	333 <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	334 <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	335 </options>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	336 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	337 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	338 <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	339 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	340 format="fasta"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	341 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	342 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	343 type="data"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	344 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	345 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	346 </conditional>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	347
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	348 <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	349
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	350 <param label="Genetic Code" name="gencode" type="select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	351 <option value="1">1. The Standard Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	352 <option value="2">2. The Vertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	353 <option value="3">3. The Yeast Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	354 <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	355 <option value="5">5. The Invertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	356 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	357 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	358 <option value="10">10. The Euplotid Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	359 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	360 <option value="12">12. The Alternative Yeast Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	361 <option value="13">13. The Ascidian Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	362 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	363 <option value="16">16. Chlorophycean Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	364 <option value="21">21. Trematode Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	365 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	366 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	367 <option value="24">24. Pterobranchia Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	368 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	369 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	370
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	371 <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	372 <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	373 <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	374 <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	375 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	376 <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	377 <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	378 <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	379 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	380 type="data"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	381 format="html" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	382 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	383 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	384
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	385 <repeat name="track_groups" title="Track Group">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	386 <param label="Track Category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	387 name="category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	388 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	389 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	390 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	391 <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	392 <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	393 <param type="select" label="Track Type" name="data_format_select">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	394 <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	395 <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	396 <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	397 <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	398 <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	399 <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	400 <!--<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	401 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	402 <when value="blast">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	403 <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	404
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	405 <param label="Features used in Blast Search"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	406 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	407 format="gff3"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	408 name="blast_parent"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	409 optional="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	410 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	411
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	412 <param label="Minimum Gap Size"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	413 help="before a new match_part feature is created"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	414 name="min_gap"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	415 type="integer"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	416 value="10"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	417 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	418 <param label="Is this a protein blast search?"
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	419 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	420 name="is_protein"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	421 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	422 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	423
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	424 <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	425
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	426 <expand macro="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	427 classname="feature"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	428 label="description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	429 description="Hit_titles"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	430 height="600px"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	431 <expand macro="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	432 token_scaling_lin_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	433 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	434 <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	435 <expand macro="track_display" />
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	436 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	437 <when value="vcf">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	438 <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	439 <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	440 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	441 <when value="gene_calls">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	442 <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	443 <conditional name="match_part" label="match/match_part data">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	444 <param label="This is match/match_part data"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	445 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	446 name="match_part_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	447 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	448 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	449 <when value="true">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	450 <param label="Match Part Feature Type"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	451 name="name"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	452 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	453 value="match"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	454 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	455 optional="False"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	456 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	457 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	458 </conditional>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	459
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	460 <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	461
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	462 <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	463 <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	464 <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	465 <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	466 <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	467 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	468 <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	469 <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	470 <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	471 name="transcriptType"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	472 type="text"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	473 value=""
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	474 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	475 optional="True"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	476 <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	477 name="subParts"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	478 type="text"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	479 value=""
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	480 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	481 optional="True"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	482 <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	483 name="impliedUTRs"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	484 type="boolean"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	485 checked="false"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	486 truevalue="true"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	487 falsevalue="false"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	488 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	489 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	490 </when>
13 69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	491 <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	492 <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	493 <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	494 name="transcriptType"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	495 type="text"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	496 value=""
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	497 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	498 optional="True"/>
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	499 </section>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	500 </when>
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	501 <when value="BlastView/View/Track/CanvasFeatures" />
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	502 </conditional>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	503 <expand macro="track_styling" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	504 <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	505 <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	506 <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	507 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	508 <when value="pileup">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	509 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	510 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	511 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	512 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	513 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	514 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	515 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	516 <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	517 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	518 <when value="wiggle">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	519 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	520
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	521 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	522 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	523 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	524 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	525 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	526 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	527 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	528 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	529 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	530 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	531 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	532 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	533
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	534 <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	535 <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	536 <option value="auto_local">Autoscale (local)</option>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	537 <option value="auto_global" selected="true">Autoscale (global)</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	538 <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	539 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	540 <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	541 <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	542 <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	543 <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	544 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	545 <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	546 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	547 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	548 </conditional>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	549 <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	550 <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	551 <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	552 </param>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	553 <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	554 <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	555 </when>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	556 <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	557 <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	558 </when>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	559 <!--
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	560 <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	561 <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	562 <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	563 <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	564 <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	565 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	566 -->
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	567 </conditional>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	568 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	569 </repeat>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	570
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	571 <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	572 <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	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="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	575 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	576 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	577 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	578 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	579
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	580 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	581 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	582 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	583
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	584 <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	585 <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	586 <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	587 <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	588 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	589 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	590
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	591 <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	592 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	593 <outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	594 <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	595 </outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	596 <tests>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	597 <test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	598 <!-- gencode -->
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	599 <param name="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	600 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	601 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	602 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	603 <param name="uglyTestingHack" value="enabled" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	604 <output name="output" file="gencode/test-1.xml" lines_diff="4" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	605 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	606 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	607 <param name="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	608 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	609 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	610 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	611 <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	612 <output name="output" file="gencode/test.xml" lines_diff="14"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	613 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	614 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	615 <param name="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	616 <param name="reference_genome\|genomes" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	617 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	618 <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	619 <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	620 <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	621 <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	622 <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	623 <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	624 <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	625 <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	626 <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	627 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	628 <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	629 <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	630 <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	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 <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	633 <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	634 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	635 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	636 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	637 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	638 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	639
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	640 <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	641 <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	642 <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	643 <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	644 <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	645 <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	646 <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	647 <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	648 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	649 <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	650 <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	651 <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	652 <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	653 <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	654 <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	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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	657 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	658 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	659 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	660 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	661
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	662 <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	663 <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	664 <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	665 <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	666 <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	667 <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	668 <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	669 <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	670 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	671 <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	672 <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	673 <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	674 <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	675 <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	676 <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	677 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	678 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	679 <param name="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	680 <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	681 <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	682 </conditional>
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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	685 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	686 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	687 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	688 <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	689 <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	690 <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	691 <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	692 <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	693 <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	694 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	695 <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	696 <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	697 <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	698 <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	699 <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	700 <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	701 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	702 <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	703 <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	704 <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	705 <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	706 <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	707 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	708 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	709 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	710 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	711 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	712 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	713 <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	714 <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	715 <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	716 <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	717 <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	718 <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	719 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	720 <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	721 <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	722 <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	723 <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	724 <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	725 <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	726 <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	727 <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	728 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	729 <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	730 <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	731 <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	732 <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	733 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	734 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	735 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	736 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	737 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	738 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	739 <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	740 <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	741 <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	742 <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	743 <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	744 <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	745 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	746 <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	747 <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	748 <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	749 <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	750 <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	751 <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	752 <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	753 <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	754 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	755 <conditional name="color_scheme">
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="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	757 <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	758 <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	759 <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	760 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	761 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	762 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	763 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	764 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	765 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	766 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	767
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	768 <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	769 <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	770 <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	771 <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	772 <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	773 <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	774 <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	775 <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	776 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	777 <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	778 <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	779 <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	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 <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	782 <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	783 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	784 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	785 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	786 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	787 <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	788 <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	789 <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	790 <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	791 <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	792 <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	793 <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	794 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	795 <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	796 <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	797 <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	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 <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	800 <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	801 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	802 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	803 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	804 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	805 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	806
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	807 <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	808 <output name="output" file="gff3/test.xml" lines_diff="64" />
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	809 </test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	810 <test>
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="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	812 <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	813 <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	814 <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	815
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	816 <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	817 <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	818 <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	819 <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	820 <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	821 <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	822 <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	823 <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	824 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	825 <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	826 <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	827 <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	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 <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	830 <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	831 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	832 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	833 <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	834 <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	835 <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	836 <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	837 <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	838 <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	839 <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	840 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	841 <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	842 <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	843 <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	844 <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	845 <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	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 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	848 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	849 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	850 <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	851 <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	852 <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	853 <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	854 <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	855 <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	856 <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	857 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	858 <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	859 <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	860 <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	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 <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	863 <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	864 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	865 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	866 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	867 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	868 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	869
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	870 <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	871 <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	872 </test>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	873 <test>
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="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	875 <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	876 <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	877 <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	878
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	879 <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	880 <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	881 <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	882 <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	883 <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	884 <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	885 <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	886 <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	887 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	888 <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	889 <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	890 <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	891 <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	892 <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	893 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	894 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	895 <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	896 <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	897 <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	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 <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	900 <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	901 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	902 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	903 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	904 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	905 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	906
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	907 <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	908 <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	909 </test>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	910 <test>
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	911 <!-- data_table -->
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	912 <param name="reference_genome\|genome_type_select" value="indexed"/>
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	913 <param name="reference_genome\|genomes" value="merlin"/>
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	914 <param name="gencode" value="1" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	915 <param name="standalone" value="Data Directory" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	916 <param name="uglyTestingHack" value="enabled" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	917 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	918 </test>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	919 </tests>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	920 <help><![CDATA[
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	921 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	922 =================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	923
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	924 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	925 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	926
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	927 Overview
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	928 --------
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	929
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	930 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	931 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	932
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	933 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	934 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	935 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	936 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	937 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	938 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	939 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	940 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	941
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	942 The JBrowse-in-Galaxy tool is maintained by `Eric
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	943 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	944 encounter missing features or bugs.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	945
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	946 Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	947 -------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	948
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	949 The first option you encounter is the Fasta Sequence(s). This option
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	950 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	951 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	952 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	953 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	954 issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	955
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	956 Standalone Instances are a somewhat in-development feature.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	957 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	958 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	959 instance. This is obviously an anti-feature because users don't want a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	960 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	961 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	962 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	963 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	964 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	965 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	966 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	967 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	968
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	969 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	970 which allows users to specify a non standard genetic code, and have
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	971 JBrowse highlight the correct start and stop codons. If you would like
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	972 to use a coding table not provided by this list, please let
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	973 `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	974 this.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	975
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	976 Track Groups represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	977 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	978 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	979
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	980 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	981
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	982 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	983 -----------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	984
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	985 Within Track Groups, you have one or more Annotation Tracks. Each
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	986 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	987 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	988 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	989 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	990 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	991 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	992
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	993 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	994 set of options:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	995
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	996 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	997 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	998
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	999 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1000 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1001 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1002 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1003 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1004
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1005 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	1006 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1007 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1008 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	1009 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	1010 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1011 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	1012 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1013
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1014 Next up is the Styling Options section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1015 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	1016 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1017 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1018
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1019 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1020
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1021 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	1022 source of the black text is configured with the style.label option,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1023 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1024 style.description option.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1025
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1026 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1027 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1028
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1029 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1030 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	1031 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1032 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1033
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1034 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1035
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1036 If you choose Ignore score, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1037 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1038 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1039 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1040 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1041 colour palette.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1042
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1043 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	1044 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1045 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1046 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1047
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1048 The linear scaling method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1049 directly to a range of output values". Logarithmic scaling says
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1050 "please take the log of the score before mapping", and Blast scaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1051 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1052 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1053 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1054 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1055 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1056
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1057 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1058 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1059 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1060
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1061 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1062 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1063 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1064 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1065
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1066 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1067 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1068
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1069 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1070 that bam data.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1071
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1072 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1073
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1074 This is strongly discouraged for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1075 Unfortunately there are no other configuration options exposed for bam
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1076 files. If you find JBrowse options you wish to see exposed, please let
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1077 `me <mailto:esr+jig@tamu.edu>`__ know.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1078
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1079 BlastXML
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1080 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1081
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1082 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1083
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1084 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1085 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1086 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1087 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1088
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1089 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	1090 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1091 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	1092 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1093 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1094 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1095 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1096 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1097 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1098 author only works on small viruses. It is strongly recommended that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1099 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1100 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1101
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1102 Protein blast search option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1103 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1104
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1105 Styling Options
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 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1109
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1110 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1111 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1112
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1113 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1114 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1115 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1116
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1117 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1118 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1119
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1120 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1121
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1122 XYPlot
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1123
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1124 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1125 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1126 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1127 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1128
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1129 Variance Band is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1130 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1131 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1132
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1133 Track Scaling is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1134 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1135 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1136 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	1137 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	1138 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	1139 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1140 autoscaling locally instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1141 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1142 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	1143 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1144 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1145
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1146 Colour Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1147 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1148
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1149 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1150 colour.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1151
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1152 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	1153
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1154 One of the more interesting options is the Bicolor pivot. This
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1155 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1156 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1157 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1158 tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1159
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1160 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1161 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1162
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1163 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1164
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1165 Known Issues
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1166 ------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1167
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1168 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1169 selector.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1170 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1171 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1172 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1173
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1174
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1175 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1176 ]]></help>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	1177 <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	1178 </tool>

Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 18:836d1aa3e89a draft