jbrowse: macros.xml annotate

annotate macros.xml @ 36:7ed0827da5a8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit e846227dfeed6e58ab8e2ee528e8fbc7c3938f86"

author	iuc
date	Sun, 26 Jan 2020 23:43:57 -0500
parents	3235aeb45c22
children	edb534491f92

rev	line source
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1 <?xml version="1.0"?>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	2 <macros>
32 6b774e9d6387 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit df0ef2f7aaf34e585edbf88654fec9dd9e6acff1 iuc parents: 31 diff changeset	3 <token name="@TOOL_VERSION@">1.16.5</token>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	4 <xml name="requirements">
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	5 <requirements>
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 17 diff changeset	6 <requirement type="package" version="@TOOL_VERSION@">jbrowse</requirement>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	7 <requirement type="package" version="2.7">python</requirement>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	8 <requirement type="package" version="1.72">biopython</requirement>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	9 <requirement type="package" version="0.6.4">bcbiogff</requirement>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	10 <requirement type="package" version="1.9">samtools</requirement>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	11 <requirement type="package" version="3.13">pyyaml</requirement>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	12 <requirement type="package" version="0.2.6">tabix</requirement>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	13 <yield/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	14 </requirements>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	15 </xml>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	16 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
35 3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279" iuc parents: 34 diff changeset	17 <token name="@WRAPPER_VERSION@">galaxy6</token>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	18 <token name="@ATTRIBUTION@"><![CDATA[
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	19 Attribution
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	20
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 32 diff changeset	21 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	22 ]]>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	23 </token>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	24
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	25 <xml name="genome_selector"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	26 token_help=""
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	27 token_label="Fasta sequences"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	28 token_optional="False" >
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	29 <conditional name="reference_genome">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	30 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	31 <option selected="True" value="indexed">Use a built-in genome</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	32 <option value="history">Use a genome from history</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	33 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	34 <when value="indexed">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	35 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	36 help="@HELP@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	37 label="@LABEL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	38 name="genomes"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	39 type="select"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	40 optional="@OPTIONAL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	41 >
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	42 <options from_data_table="all_fasta">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	43 <filter column="2" type="sort_by" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	44 <validator message="No genomes are available for the selected input dataset" type="no_options" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	45 </options>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	46 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	47 </when>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	48 <when value="history">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	49 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	50 format="fasta"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	51 label="@LABEL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	52 help="@HELP@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	53 name="genomes"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	54 type="data"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	55 optional="@OPTIONAL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	56 multiple="True" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	57 </when>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	58 </conditional>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	59 </xml>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	60
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	61 <xml name="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	62 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	63 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	64 token_select_label="Color Specification"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	65 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	66 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	67 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	68 <conditional name="@COND_NAME@" label="@COND_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	69 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	70 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	71 <option value="manual">@MANUAL_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	72 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	73 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	74 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	75 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	76 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	77 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	78 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	79 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	80
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	81 <xml name="track_display">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	82 <param type="select" label="Track Visibility" name="track_visibility">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	83 <option value="default_off">Off for new users</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	84 <option value="default_on">On for new users</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	85 <option value="force">Force On</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	86 <option value="always">Always On (ignores URL parameters)</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	87 </param>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	88 <param type="select" label="Override Apollo Plugins" name="override_apollo_plugins" help="Disable the apollo plugin for this track, this disables the ability to make an annotation from this feature.">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	89 <option value="True">Yes - Override</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	90 <option value="False" selected="True">No - Do not Override</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	91 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	92 <param type="select" label="Override Apollo Draggability" name="override_apollo_drag" help="Disable apollo's drag-to-create feature functionality.">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	93 <option value="True">Yes - Override</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	94 <option value="False" selected="True">No - Do not Override</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	95 </param>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	96 </xml>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	97
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	98 <xml name="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	99 token_label="JBrowse style.color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	100 token_name="style_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	101 token_value="goldenrod"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	102 token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	103 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	104 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	105 <sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	106 <valid initial="string.letters,string.digits">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	107 <add value="#" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	108 </valid>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	109 </sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	110 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	111 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	112
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	113 <xml name="auto_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	114 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	115 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	116 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	117 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	118 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	119 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	120 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	121 cond_label="@COND_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	122 cond_name="@COND_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	123 select_label="@SELECT_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	124 select_name="@SELECT_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	125 automatic_label="@AUTOMATIC_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	126 manual_label="@MANUAL_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	127 <expand macro="jb_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	128 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	129 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	130 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	131
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	132
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	133
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	134 <xml name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	135 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	136 <option value="BrBg">BrBg: Brown - Blue Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	137 <option value="PiYg">PiYg: Pink - Yellow Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	138 <option value="PRGn">PRGn: Purple Red - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	139 <option value="PuOr">PuOr: Purple - Orange</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	140 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	141 <option value="RdGy">RdGy: Red - Gray</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	142 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	143 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	144 <option value="Spectral">Spectral</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	145 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	146 </xml>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	147 <xml name="general_options">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	148 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	149 <param label="Default Location" type="text" name="defaultLocation" value="" help="Initial location to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	150 <param label="Track Padding" type="integer" value="20" name="trackPadding" help="Spacing between tracks in the genome view, in pixels." />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	151
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	152 <param label="Enable Share Link" name="shareLink" type="boolean" checked="true" truevalue="true" falsevalue="false" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	153 <param label="About the Browser" type="text" name="aboutDescription" value="" help="Description of the browser to be used in the 'About' popup" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	154
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	155 <param label="Show Track List" name="show_tracklist" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the track list"/>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	156 <param label="Show Navigation" name="show_nav" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the navigation menu"/>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	157 <param label="Show Overview" name="show_overview" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the overview bar"/>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	158 <param label="Show Menu" name="show_menu" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the menu bar"/>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	159
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	160 <param label="Hide Genome Options" name="hideGenomeOptions" type="boolean" truevalue="true" falsevalue="false" help="Hide options for opening a sequence file"/>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	161 </section>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	162 </xml>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	163 <xml name="color_selection_minmax">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	164 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	165 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	166 auto case as well, but may be safe to just say "brewer colors? Pff,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	167 red/blue" -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	168 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	169 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	170 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	171 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	172 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	173 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	174 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	175 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	176 label="JBrowse style.pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	177 name="style_pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	178 value="blue"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	179 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	180 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	181 label="JBrowse style.neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	182 name="style_neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	183 value="red"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	184 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	185 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	186
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	187 <conditional name="bicolor_pivot" label="Bicolor Pivot">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	188 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	189 <option value="zero" selected="true">Zero</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	190 <option value="mean">Mean</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	191 <option value="custom">Custom Value</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	192 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	193 <when value="zero" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	194 <when value="mean" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	195 <when value="custom">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	196 <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	197 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	198 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	199 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	200 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	201
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	202 <xml name="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	203 token_scaling_lin_select="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	204 token_scaling_log_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	205 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	206 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	207 <conditional name="color_score" label="JBrowse style.color & Score relationship">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	208 <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	209 <option value="score">Based on score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	210 <option value="none" selected="true">Ignore score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	211 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	212 <when value="none">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	213 <!-- When no scaling is done, no scores available, then just let the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	214 user choose a base color for the track -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	215 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	216 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	217 <when value="score">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	218 <!-- Scaling -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	219 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	220 help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	221 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	222 <option value="logarithmic" selected="false">Logarithmic scaling</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	223 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	224 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	225
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	226 <!-- Scaling Bounds -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	227 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	228 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	229 <option value="automatic" selected="true">Automatically determined</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	230 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	231 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	232 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	233 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	234 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	235 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	236 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	237 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	238 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	239
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	240 <!-- Scale color -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	241 <conditional name="color_scheme" label="Color Scheme for scored features">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	242 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	243 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	244 <!--<option value="brewer">Brewer Color Schemes</option>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	245 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	246 <when value="opacity">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	247 <!-- Single color selection mode -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	248 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	249 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	250 <!--<when value="brewer">-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	251 <!--[> Brewer continuum selection <]-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	252 <!--<expand macro="brewer_scheme" />-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	253 <!--</when>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	254 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	255 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	256 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	257 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	258 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	259 <xml name="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	260 token_classname="feature"
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	261 token_label="product,name,id"
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	262 token_description="note,description"
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	263 token_height="10px"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	264 token_maxheight="600">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	265 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	266 <param label="JBrowse style.className" type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	267 name="style_classname"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	268 value="@CLASSNAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	269 help="Set CSS style.className property"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	270 <param label="JBrowse style.label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	271 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	272 name="style_label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	273 value="@LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	274 help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	275 <param label="JBrowse style.description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	276 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	277 name="style_description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	278 value="@DESCRIPTION@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	279 help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	280 <param label="JBrowse style.height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	281 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	282 name="style_height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	283 value="@HEIGHT@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	284 help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	285 <param label="JBrowse maxHeight"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	286 type="text"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	287 name="max_height"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	288 value="@MAXHEIGHT@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	289 help="Maximum height that the track is permitted to reach in pixels."/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	290 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	291 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	292
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	293 <xml name="track_custom_config">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	294 <section name="jb_custom_config" title="JBrowse Custom Track Config [Advanced]" expanded="false">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	295 <repeat name="option" title="Custom Track Config Option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	296 <param name="opt_key" type="text" label="Key for JBrowse track config option"
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	297 help="Multilevel keys (e.g., 'style.label') are delimited by a period character ('.').">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	298 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w]+(\.\w+)*$</validator>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	299 </param>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	300 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	301 <param name="val_type" type="select" label="Choose the type of value for the option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	302 <option value="text" selected="true">Text</option>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	303 <option value="integer">Integer number</option>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	304 <option value="float">Floating point number</option>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	305 <option value="boolean">Boolean</option>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	306 </param>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	307 <when value="text">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	308 <param name="val" type="text" label="Value for custom track option."
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	309 help="Will override other track options set elsewhere.">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	310 <validator type="empty_field" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	311 </param>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	312 </when>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	313 <when value="integer">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	314 <param name="val" type="integer" value="0" label="Value for custom track option."
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	315 help="Will override other track options set elsewhere." />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	316 </when>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	317 <when value="float">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	318 <param name="val" type="float" value="0" label="Value for custom track option."
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	319 help="Will override other track options set elsewhere." />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	320 </when>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	321 <when value="boolean">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	322 <param name="val" type="boolean" truevalue="true" falsevalue="false"
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	323 label="Value for custom track option."
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	324 help="Will override other track options set elsewhere." />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	325 </when>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	326 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	327 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	328 </section>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	329 </xml>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	330
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	331 <xml 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	332 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	333 <repeat name="track_menu" title="Track Menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	334 <param label="Menu action"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	335 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	336 name="menu_action"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	337 help="Action performed when user clicks on the menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	338 <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	339 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	340 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	341 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	342 <param label="Menu label"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	343 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	344 name="menu_label"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	345 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	346 <expand macro="menu_sanitize" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	347 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	348 <param label="Menu title"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	349 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	350 name="menu_title"
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	351 help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	352 <expand macro="menu_sanitize" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	353 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	354 <param label="Menu url"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	355 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	356 name="menu_url"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	357 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	358 <expand macro="menu_sanitize" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	359 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	360 <param label="Menu icon"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	361 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	362 name="menu_icon"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	363 help="Icon to display next to menu label">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	364 <option value="dijitIconBookmark" selected="true">Bookmark</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	365 <option value="dijitIconSave">Save</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	366 <option value="dijitIconPrint">Print</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	367 <option value="dijitIconCut">Cut</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	368 <option value="dijitIconCopy">Copy</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	369 <option value="dijitIconClear">Clear</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	370 <option value="dijitIconDelete">Delete</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	371 <option value="dijitIconUndo">Undo</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	372 <option value="dijitIconEdit">Edit</option>
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="dijitIconNewTask">New Task</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="dijitIconEditTask">Edit Task</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	375 <option value="dijitIconEditProperty">Edit Property</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	376 <option value="dijitIconTask">Task</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	377 <option value="dijitIconFilter">Filter</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	378 <option value="dijitIconConfigure">Configure</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	379 <option value="dijitIconSearch">Search</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	380 <option value="dijitIconApplication">Application</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	381 <option value="dijitIconChart">Chart</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	382 <option value="dijitIconConnector">Connector</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	383 <option value="dijitIconDatabase">Database</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	384 <option value="dijitIconDocuments">Documents</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	385 <option value="dijitIconMail">Mail</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	386 <option value="dijitLeaf">Leaf</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	387 <option value="dijitIconFile">File</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	388 <option value="dijitIconFunction">Function</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	389 <option value="dijitIconKey">Key</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	390 <option value="dijitIconPackage">Package</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	391 <option value="dijitIconSample">Sample</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	392 <option value="dijitIconTable">Table</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	393 <option value="dijitIconUsers">Users</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	394 <option value="dijitIconFolderClosed">Folder Closed</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	395 <option value="dijitIconFolderOpen">Folder Open</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	396 <option value="dijitIconError">Error</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	397 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	398 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	399 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	400 </xml>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	401
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	402 <xml name="menu_sanitize">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	403 <sanitizer>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	404 <valid>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	405 <add value="{"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	406 <add value="}"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	407 <add value="!"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	408 <add value="?"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	409 <add value="&"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	410 <add value="+"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	411 <add value="="/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	412 <add value="'"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	413 <add value='"'/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	414 </valid>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	415 </sanitizer>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	416 </xml>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	417
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	418 <xml name="input_conditional" token_label="Track Data" token_format="data">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	419 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	420 </xml>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	421 <xml name="citations">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	422 <citations>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	423 <citation type="doi">10.1101/gr.094607.109</citation>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	424 </citations>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	425 </xml>
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	426
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	427 <xml name="canvas_options">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	428 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	429 <param label="Transcript type"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	430 name="transcriptType"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	431 type="text"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	432 value=""
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	433 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	434 optional="True"/>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	435 <param label="Subfeatures type"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	436 name="subParts"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	437 type="text"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	438 value=""
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	439 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	440 optional="True"/>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	441 <param label="Implied UTRs"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	442 name="impliedUTRs"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	443 type="boolean"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	444 checked="false"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	445 truevalue="true"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	446 falsevalue="false"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	447 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"/>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	448 </section>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	449 </xml>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	450
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	451 <xml name="html_options">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	452 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	453 <param label="Top level features"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	454 name="topLevelFeatures"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	455 type="text"
30 ca2def38369c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977 iuc parents: 28 diff changeset	456 help="Select which top level features should be displayed. If empty, will try to display all features. If your input files represents gene→mRNA→exon/CDS/UTR, you should use mRNA if exons don't render."
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	457 optional="True"/>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	458 </section>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	459 </xml>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	460 </macros>

Mercurial > repos > iuc > jbrowse

annotate macros.xml @ 36:7ed0827da5a8 draft