jbrowse: macros.xml annotate

annotate macros.xml @ 23:dba3c47e1798 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958

author	iuc
date	Wed, 12 Dec 2018 02:54:31 -0500
parents	1c718d8b3532
children	fa30df9b79c2

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>
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 17 diff changeset	3 <token name="@TOOL_VERSION@">1.12.5</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>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	8 <requirement type="package" version="1.66">biopython</requirement>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	9 <requirement type="package" version="0.6.2">bcbiogff</requirement>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	10 <requirement type="package" version="1.2">samtools</requirement>
2 b6a0e126dbee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a9cedb0983cc262cfdac04464566fdded884318b iuc parents: 1 diff changeset	11 <requirement type="package" version="3.11">pyyaml</requirement>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	12 <yield/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	13 </requirements>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	14 </xml>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	15 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
23 dba3c47e1798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958 iuc parents: 21 diff changeset	16 <token name="@WRAPPER_VERSION@">galaxy2</token>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	17 <xml name="stdio">
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	18 <stdio>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	19 <exit_code range="1:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	20 <exit_code range=":-1"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	21 <regex match="Error:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	22 <regex match="Exception:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	23 </stdio>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	24 </xml>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	25 <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	26 Attribution
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	27
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	28 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	29 ]]>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	30 </token>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	31
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	32 <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	33 token_help=""
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	34 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	35 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	36 <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	37 <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	38 <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	39 <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	40 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	41 <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	42 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	43 help="@HELP@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	44 label="@LABEL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	45 name="genomes"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	46 type="select"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	47 optional="@OPTIONAL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	48 >
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	49 <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	50 <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	51 <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	52 </options>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	53 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	54 </when>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	55 <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	56 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	57 format="fasta"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	58 label="@LABEL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	59 help="@HELP@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	60 name="genomes"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	61 type="data"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	62 optional="@OPTIONAL@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	63 multiple="True" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	64 </when>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	65 </conditional>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	66 </xml>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	67
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	68 <xml name="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	69 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	70 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	71 token_select_label="Color Specification"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	72 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	73 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	74 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	75 <conditional name="@COND_NAME@" label="@COND_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	76 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	77 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	78 <option value="manual">@MANUAL_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	79 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	80 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	81 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	82 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	83 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	84 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	85 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	86 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	87
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	88 <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	89 <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	90 <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	91 <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	92 <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	93 <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	94 </param>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	95 <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	96 <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	97 <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	98 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	99 <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	100 <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	101 <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	102 </param>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	103 </xml>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	104
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	105 <xml name="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	106 token_label="JBrowse style.color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	107 token_name="style_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	108 token_value="goldenrod"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	109 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	110 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	111 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	112 <sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	113 <valid initial="string.letters,string.digits">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	114 <add value="#" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	115 </valid>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	116 </sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	117 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	118 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	119
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	120 <xml name="auto_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	121 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	122 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	123 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	124 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	125 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	126 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	127 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	128 cond_label="@COND_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	129 cond_name="@COND_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	130 select_label="@SELECT_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	131 select_name="@SELECT_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	132 automatic_label="@AUTOMATIC_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	133 manual_label="@MANUAL_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	134 <expand macro="jb_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	135 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	136 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	137 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	138
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	139
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	140
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	141 <xml name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	142 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	143 <option value="BrBg">BrBg: Brown - Blue Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	144 <option value="PiYg">PiYg: Pink - Yellow Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	145 <option value="PRGn">PRGn: Purple Red - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	146 <option value="PuOr">PuOr: Purple - Orange</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	147 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	148 <option value="RdGy">RdGy: Red - Gray</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	149 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	150 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	151 <option value="Spectral">Spectral</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	152 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	153 </xml>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	154 <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	155 <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	156 <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	157 <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	158
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	159 <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	160 <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	161
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	162 <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	163 <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	164 <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	165 <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	166
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	167 <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	168 </section>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	169 </xml>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	170 <xml name="color_selection_minmax">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	171 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	172 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	173 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	174 red/blue" -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	175 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	176 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	177 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	178 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	179 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	180 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	181 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	182 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	183 label="JBrowse style.pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	184 name="style_pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	185 value="blue"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	186 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	187 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	188 label="JBrowse style.neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	189 name="style_neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	190 value="red"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	191 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	192 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	193
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	194 <conditional name="bicolor_pivot" label="Bicolor Pivot">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	195 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	196 <option value="zero" selected="true">Zero</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	197 <option value="mean">Mean</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	198 <option value="custom">Custom Value</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	199 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	200 <when value="zero" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	201 <when value="mean" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	202 <when value="custom">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	203 <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	204 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	205 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	206 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	207 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	208
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	209 <xml name="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	210 token_scaling_lin_select="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	211 token_scaling_log_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	212 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	213 <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	214 <conditional name="color_score" label="JBrowse style.color & Score relationship">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	215 <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	216 <option value="score">Based on score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	217 <option value="none" selected="true">Ignore score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	218 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	219 <when value="none">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	220 <!-- When no scaling is done, no scores available, then just let the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	221 user choose a base color for the track -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	222 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	223 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	224 <when value="score">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	225 <!-- Scaling -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	226 <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	227 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	228 <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	229 <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	230 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
3 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
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	233 <!-- Scaling Bounds -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	234 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	235 <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	236 <option value="automatic" selected="true">Automatically determined</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	237 <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	238 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	239 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	240 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	241 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	242 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	243 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	244 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	245 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	246
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	247 <!-- Scale color -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	248 <conditional name="color_scheme" label="Color Scheme for scored features">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	249 <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	250 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	251 <!--<option value="brewer">Brewer Color Schemes</option>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	252 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	253 <when value="opacity">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	254 <!-- Single color selection mode -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	255 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	256 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	257 <!--<when value="brewer">-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	258 <!--[> Brewer continuum selection <]-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	259 <!--<expand macro="brewer_scheme" />-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	260 <!--</when>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	261 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	262 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	263 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	264 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	265 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	266 <xml name="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	267 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	268 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	269 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	270 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	271 token_maxheight="600">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	272 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	273 <param label="JBrowse style.className" type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	274 name="style_classname"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	275 value="@CLASSNAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	276 help="Set CSS style.className property"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	277 <param label="JBrowse style.label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	278 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	279 name="style_label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	280 value="@LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	281 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	282 <param label="JBrowse style.description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	283 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	284 name="style_description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	285 value="@DESCRIPTION@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	286 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	287 <param label="JBrowse style.height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	288 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	289 name="style_height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	290 value="@HEIGHT@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	291 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	292 <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	293 type="text"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	294 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	295 value="@MAXHEIGHT@"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 15 diff changeset	296 help="Maximum height that the track is permitted to reach in pixels."/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	297 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	298 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	299
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	300 <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	301 <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	302 <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	303 <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	304 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	305 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	306 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	307 <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	308 <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	309 <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	310 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	311 <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	312 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	313 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	314 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	315 <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	316 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	317 <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	318 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	319 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	320 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	321 <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	322 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	323 <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	324 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	325 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	326 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	327 <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	328 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	329 <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	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 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	332 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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	367 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	368 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	369 </xml>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	370
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	371 <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	372 <sanitizer>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	373 <valid>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	374 <add value="{"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	375 <add value="}"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	376 <add value="!"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	377 <add value="?"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	378 <add value="&"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	379 <add value="+"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	380 <add value="="/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	381 <add value="'"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	382 <add value='"'/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	383 </valid>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	384 </sanitizer>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	385 </xml>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	386
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	387 <xml name="input_conditional" token_label="Track Data" token_format="data">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	388 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	389 </xml>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	390 <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	391 <citations>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	392 <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	393 </citations>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	394 </xml>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	395 </macros>

Mercurial > repos > iuc > jbrowse

annotate macros.xml @ 23:dba3c47e1798 draft