jbrowse: macros.xml annotate

annotate macros.xml @ 15:4e11a688a635 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit d7f7217983bfd655b8af5795d9330aef27e2bd7f

author	iuc
date	Wed, 14 Jun 2017 17:21:28 -0400
parents	1a6d882d340d
children	ff11d442feed

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>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	3 <xml name="requirements">
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	4 <requirements>
15 4e11a688a635 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit d7f7217983bfd655b8af5795d9330aef27e2bd7f iuc parents: 10 diff changeset	5 <requirement type="package" version="1.12.3">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	6 <requirement type="package" version="2.7">python</requirement>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	7 <requirement type="package" version="1.66">biopython</requirement>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	8 <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	9 <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	10 <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	11 <yield/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	12 </requirements>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	13 </xml>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	14 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
15 4e11a688a635 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit d7f7217983bfd655b8af5795d9330aef27e2bd7f iuc parents: 10 diff changeset	15 <token name="@WRAPPER_VERSION@">0.5.3</token>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	16 <xml name="stdio">
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	17 <stdio>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	18 <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	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 <regex match="Error:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	21 <regex match="Exception:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	22 </stdio>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	23 </xml>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	24 <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	25 Attribution
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	26
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	27 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	28 ]]>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	29 </token>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	30 <xml name="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	31 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	32 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	33 token_select_label="Color Specification"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	34 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	35 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	36 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	37 <conditional name="@COND_NAME@" label="@COND_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	38 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	39 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	40 <option value="manual">@MANUAL_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	41 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	42 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	43 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	44 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	45 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	46 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	47 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	48 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	49
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	50 <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	51 <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	52 <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	53 <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	54 <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	55 <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	56 </param>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	57 </xml>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	58
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	59 <xml name="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	60 token_label="JBrowse style.color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	61 token_name="style_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	62 token_value="goldenrod"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	63 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	64 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	65 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	66 <sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	67 <valid initial="string.letters,string.digits">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	68 <add value="#" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	69 </valid>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	70 </sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	71 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	72 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	73
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	74 <xml name="auto_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	75 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	76 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	77 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	78 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	79 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	80 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	81 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	82 cond_label="@COND_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	83 cond_name="@COND_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	84 select_label="@SELECT_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	85 select_name="@SELECT_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	86 automatic_label="@AUTOMATIC_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	87 manual_label="@MANUAL_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	88 <expand macro="jb_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	89 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	90 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	91 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	92
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	93
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	94
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	95 <xml name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	96 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	97 <option value="BrBg">BrBg: Brown - Blue Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	98 <option value="PiYg">PiYg: Pink - Yellow Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	99 <option value="PRGn">PRGn: Purple Red - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	100 <option value="PuOr">PuOr: Purple - Orange</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	101 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	102 <option value="RdGy">RdGy: Red - Gray</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	103 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	104 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	105 <option value="Spectral">Spectral</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	106 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	107 </xml>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	108 <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	109 <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	110 <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	111 <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	112
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	113 <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	114 <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	115
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	116 <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	117 <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	118 <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	119 <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	120
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	121 <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	122 </section>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	123 </xml>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	124 <xml name="color_selection_minmax">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	125 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	126 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	127 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	128 red/blue" -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	129 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	130 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	131 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	132 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	133 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	134 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	135 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	136 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	137 label="JBrowse style.pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	138 name="style_pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	139 value="blue"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	140 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	141 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	142 label="JBrowse style.neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	143 name="style_neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	144 value="red"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	145 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	146 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	147
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	148 <conditional name="bicolor_pivot" label="Bicolor Pivot">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	149 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	150 <option value="zero" selected="true">Zero</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	151 <option value="mean">Mean</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	152 <option value="custom">Custom Value</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	153 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	154 <when value="zero" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	155 <when value="mean" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	156 <when value="custom">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	157 <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	158 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	159 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	160 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	161 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	162
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	163 <xml name="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	164 token_scaling_lin_select="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	165 token_scaling_log_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	166 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	167 <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	168 <conditional name="color_score" label="JBrowse style.color & Score relationship">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	169 <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	170 <option value="score">Based on score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	171 <option value="none" selected="true">Ignore score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	172 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	173 <when value="none">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	174 <!-- When no scaling is done, no scores available, then just let the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	175 user choose a base color for the track -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	176 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	177 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	178 <when value="score">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	179 <!-- Scaling -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	180 <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	181 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.">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	182 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	183 <option value="logarithmic">Logarithmic scaling</option>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	184 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	185 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	186
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	187 <!-- Scaling Bounds -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	188 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	189 <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	190 <option value="automatic" selected="true">Automatically determined</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	191 <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	192 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	193 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	194 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	195 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	196 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	197 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	198 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	199 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	200
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	201 <!-- Scale color -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	202 <conditional name="color_scheme" label="Color Scheme for scored features">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	203 <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	204 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	205 <!--<option value="brewer">Brewer Color Schemes</option>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	206 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	207 <when value="opacity">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	208 <!-- Single color selection mode -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	209 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	210 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	211 <!--<when value="brewer">-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	212 <!--[> Brewer continuum selection <]-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	213 <!--<expand macro="brewer_scheme" />-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	214 <!--</when>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	215 </conditional>
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 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	218 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	219 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	220 <xml name="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	221 token_classname="feature"
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	222 token_label="name,id"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	223 token_description="note,description"
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	224 token_height="100px">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	225 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	226 <param label="JBrowse style.className" type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	227 name="style_classname"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	228 value="@CLASSNAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	229 help="Set CSS style.className property"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	230 <param label="JBrowse style.label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	231 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	232 name="style_label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	233 value="@LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	234 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	235 <param label="JBrowse style.description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	236 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	237 name="style_description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	238 value="@DESCRIPTION@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	239 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	240 <param label="JBrowse style.height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	241 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	242 name="style_height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	243 value="@HEIGHT@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	244 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."/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	245 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	246 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	247
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	248 <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	249 <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	250 <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	251 <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	252 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	253 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	254 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	255 <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	256 <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	257 <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	258 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	259 <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	260 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	261 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	262 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	263 <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	264 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	265 <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	266 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	267 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	268 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	269 <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	270 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	271 <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	272 type="text"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	273 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	274 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	275 <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	276 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	277 <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	278 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	279 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	280 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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	315 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	316 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	317 </xml>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	318
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	319 <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	320 <sanitizer>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	321 <valid>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	322 <add value="{"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	323 <add value="}"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	324 <add value="!"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	325 <add value="?"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	326 <add value="&"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	327 <add value="+"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	328 <add value="="/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	329 <add value="'"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	330 <add value='"'/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	331 </valid>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	332 </sanitizer>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	333 </xml>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	334
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	335 <xml name="input_conditional" token_label="Track Data" token_format="data">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	336 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	337 </xml>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	338 <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	339 <citations>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	340 <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	341 </citations>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	342 </xml>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	343 </macros>

Mercurial > repos > iuc > jbrowse

annotate macros.xml @ 15:4e11a688a635 draft