jbrowse: macros.xml annotate

annotate macros.xml @ 42:c1451868f8d4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975

author	iuc
date	Thu, 08 Jun 2017 17:31:17 -0400
parents	d5e8d72c432a
children	976731ca823c

rev	line source
0 c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	1 <?xml version="1.0"?>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	2 <macros>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	3 <xml name="requirements">
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	4 <requirements>
42 c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	5 <requirement type="package" version="1.12.1">jbrowse</requirement>
13 67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty iuc parents: 12 diff changeset	6 <requirement type="package" version="2.7">python</requirement>
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	7 <requirement type="package" version="1.66">biopython</requirement>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	8 <requirement type="package" version="0.6.2">bcbiogff</requirement>
13 67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty iuc parents: 12 diff changeset	9 <requirement type="package" version="1.2">samtools</requirement>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty iuc parents: 12 diff changeset	10 <requirement type="package" version="3.11">pyyaml</requirement>
0 c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	11 <yield/>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	12 </requirements>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	13 </xml>
42 c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	14 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	15 <token name="@WRAPPER_VERSION@">0.5.2</token>
0 c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	16 <xml name="stdio">
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	17 <stdio>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	18 <exit_code range="1:"/>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	19 <exit_code range=":-1"/>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	20 <regex match="Error:"/>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	21 <regex match="Exception:"/>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	22 </stdio>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	23 </xml>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	24 <token name="@ATTRIBUTION@"><![CDATA[
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	25 Attribution
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	26
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	27 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
0 c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	28 ]]>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	29 </token>
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	30 <xml name="auto_manual_tk"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	31 token_cond_label="Color"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	32 token_cond_name="color"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	33 token_select_label="Color Specification"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	34 token_select_name="color_select"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	35 token_automatic_label="Automatically selected"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	36 token_manual_label="Manual Color Selection">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	37 <conditional name="@COND_NAME@" label="@COND_LABEL@">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	38 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	39 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	40 <option value="manual">@MANUAL_LABEL@</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	41 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	42 <when value="automatic">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	43 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	44 <when value="manual">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	45 <yield />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	46 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	47 </conditional>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	48 </xml>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	49
30 12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	50 <xml name="track_display">
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	51 <param type="select" label="Track Visibility" name="track_visibility">
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	52 <option value="default_off">Off for new users</option>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	53 <option value="default_on">On for new users</option>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	54 <option value="force">Force On</option>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	55 <option value="always">Always On (ignores URL parameters)</option>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	56 </param>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	57 </xml>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	58
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	59 <xml name="jb_color"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	60 token_label="JBrowse style.color"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	61 token_name="style_color"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	62 token_value="goldenrod"
318a0aa5075a Uploaded manually iuc parents: 13 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"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	64 >
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	65 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	66 <sanitizer>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	67 <valid initial="string.letters,string.digits">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	68 <add value="#" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	69 </valid>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	70 </sanitizer>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	71 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	72 </xml>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	73
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	74 <xml name="auto_color"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	75 token_cond_label="Color"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	76 token_cond_name="color"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	77 token_select_label="Color Selection"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	78 token_select_name="color_select"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	79 token_automatic_label="Automatically selected"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	80 token_manual_label="Manual Color Selection">
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	81 <expand macro="auto_manual_tk"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	82 cond_label="@COND_LABEL@"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	83 cond_name="@COND_NAME@"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	84 select_label="@SELECT_LABEL@"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	85 select_name="@SELECT_NAME@"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	86 automatic_label="@AUTOMATIC_LABEL@"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	87 manual_label="@MANUAL_LABEL@">
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	88 <expand macro="jb_color" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	89 <yield />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	90 </expand>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	91 </xml>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	92
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	93
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	94
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	95 <xml name="brewer_scheme">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	96 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	97 <option value="BrBg">BrBg: Brown - Blue Green</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	98 <option value="PiYg">PiYg: Pink - Yellow Green</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	99 <option value="PRGn">PRGn: Purple Red - Green</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	100 <option value="PuOr">PuOr: Purple - Orange</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	101 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	102 <option value="RdGy">RdGy: Red - Gray</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	103 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	104 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	105 <option value="Spectral">Spectral</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	106 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	107 </xml>
30 12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	108 <xml name="general_options">
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	109 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 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'"/>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	111 <param label="Track Padding" type="integer" value="20" name="trackPadding" help="Spacing between tracks in the genome view, in pixels." />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	112
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	113 <param label="Enable Share Link" name="shareLink" type="boolean" checked="true" truevalue="true" falsevalue="false" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 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" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	115
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 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"/>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	117 <param label="Show Navigation" name="show_nav" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the navigation menu"/>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	118 <param label="Show Overview" name="show_overview" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the overview bar"/>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	119 <param label="Show Menu" name="show_menu" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the menu bar"/>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	120
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	121 <param label="Hide Genome Options" name="hideGenomeOptions" type="boolean" truevalue="true" falsevalue="false" help="Hide options for opening a sequence file"/>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	122 </section>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 29 diff changeset	123 </xml>
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	124 <xml name="color_selection_minmax">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	125 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	126 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	127 auto case as well, but may be safe to just say "brewer colors? Pff,
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	128 red/blue" -->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	129 <expand macro="auto_manual_tk"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	130 token_cond_label="Color"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	131 token_cond_name="color"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	132 token_select_label="Color Selection"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	133 token_select_name="color_select"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	134 token_automatic_label="Automatically selected"
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	135 token_manual_label="Manual Color Selection">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	136 <expand macro="jb_color"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	137 label="JBrowse style.pos_color"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	138 name="style_pos_color"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	139 value="blue"
5614cf75bb24 Uploaded iuc parents: 26 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." />
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	141 <expand macro="jb_color"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	142 label="JBrowse style.neg_color"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	143 name="style_neg_color"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	144 value="red"
5614cf75bb24 Uploaded iuc parents: 26 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." />
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	146 </expand>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	147
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	148 <conditional name="bicolor_pivot" label="Bicolor Pivot">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	149 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	150 <option value="zero" selected="true">Zero</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	151 <option value="mean">Mean</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	152 <option value="custom">Custom Value</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	153 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	154 <when value="zero" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	155 <when value="mean" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	156 <when value="custom">
318a0aa5075a Uploaded manually iuc parents: 13 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." />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	158 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	159 </conditional>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	160 </section>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	161 </xml>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	162
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	163 <xml name="color_selection"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	164 token_scaling_lin_select="true"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	165 token_scaling_log_select="false"
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	166 >
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	167 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	168 <conditional name="color_score" label="JBrowse style.color & Score relationship">
318a0aa5075a Uploaded manually iuc parents: 13 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">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	170 <option value="score">Based on score</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	171 <option value="none" selected="true">Ignore score</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	172 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	173 <when value="none">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	174 <!-- When no scaling is done, no scores available, then just let the
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	175 user choose a base color for the track -->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	176 <expand macro="auto_color" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	177 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	178 <when value="score">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	179 <!-- Scaling -->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	180 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
29 5614cf75bb24 Uploaded iuc parents: 26 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.">
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	182 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
42 c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	183 <option value="logarithmic">Logarithmic scaling</option>
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	184 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	185 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	186
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	187 <!-- Scaling Bounds -->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	188 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	189 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	190 <option value="automatic" selected="true">Automatically determined</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	191 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	192 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	193 <when value="automatic">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	194 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	195 <when value="manual">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	196 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	197 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	198 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	199 </conditional>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	200
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	201 <!-- Scale color -->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	202 <conditional name="color_scheme" label="Color Scheme for scored features">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	203 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	204 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	205 <!--<option value="brewer">Brewer Color Schemes</option>-->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	206 </param>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	207 <when value="opacity">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	208 <!-- Single color selection mode -->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	209 <expand macro="auto_color" />
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	210 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	211 <!--<when value="brewer">-->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	212 <!--[> Brewer continuum selection <]-->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	213 <!--<expand macro="brewer_scheme" />-->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	214 <!--</when>-->
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	215 </conditional>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	216 </when>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	217 </conditional>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	218 </section>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	219 </xml>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	220 <xml name="track_styling"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	221 token_classname="feature"
42 c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	222 token_label="name,id"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	223 token_description="note,description"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	224 token_height="100px">
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	225 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	226 <param label="JBrowse style.className" type="text"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	227 name="style_classname"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	228 value="@CLASSNAME@"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	229 help="Set CSS style.className property"/>
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	230 <param label="JBrowse style.label"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	231 type="text"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	232 name="style_label"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	233 value="@LABEL@"
5614cf75bb24 Uploaded iuc parents: 26 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'" />
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	235 <param label="JBrowse style.description"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	236 type="text"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	237 name="style_description"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	238 value="@DESCRIPTION@"
5614cf75bb24 Uploaded iuc parents: 26 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."/>
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	240 <param label="JBrowse style.height"
29 5614cf75bb24 Uploaded iuc parents: 26 diff changeset	241 type="text"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	242 name="style_height"
5614cf75bb24 Uploaded iuc parents: 26 diff changeset	243 value="@HEIGHT@"
5614cf75bb24 Uploaded iuc parents: 26 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."/>
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	245 </section>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	246 </xml>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	247
42 c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	248 <xml name="track_menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	249 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	250 <repeat name="track_menu" title="Track Menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	251 <param label="Menu action"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	252 type="select"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	253 name="menu_action"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	254 help="Action performed when user clicks on the menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 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>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	256 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	257 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	258 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	259 <param label="Menu label"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	260 type="text"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	261 name="menu_label"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	262 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	263 <expand macro="menu_sanitize" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	264 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	265 <param label="Menu title"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	266 type="text"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	267 name="menu_title"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	268 help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	269 <expand macro="menu_sanitize" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	270 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	271 <param label="Menu url"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	272 type="text"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	273 name="menu_url"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	274 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	275 <expand macro="menu_sanitize" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	276 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	277 <param label="Menu icon"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	278 type="select"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	279 name="menu_icon"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	280 help="Icon to display next to menu label">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	281 <option value="dijitIconBookmark" selected="true">Bookmark</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	282 <option value="dijitIconSave">Save</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	283 <option value="dijitIconPrint">Print</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	284 <option value="dijitIconCut">Cut</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	285 <option value="dijitIconCopy">Copy</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	286 <option value="dijitIconClear">Clear</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	287 <option value="dijitIconDelete">Delete</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	288 <option value="dijitIconUndo">Undo</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	289 <option value="dijitIconEdit">Edit</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	290 <option value="dijitIconNewTask">New Task</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	291 <option value="dijitIconEditTask">Edit Task</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	292 <option value="dijitIconEditProperty">Edit Property</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	293 <option value="dijitIconTask">Task</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	294 <option value="dijitIconFilter">Filter</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	295 <option value="dijitIconConfigure">Configure</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	296 <option value="dijitIconSearch">Search</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	297 <option value="dijitIconApplication">Application</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	298 <option value="dijitIconChart">Chart</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	299 <option value="dijitIconConnector">Connector</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	300 <option value="dijitIconDatabase">Database</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	301 <option value="dijitIconDocuments">Documents</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	302 <option value="dijitIconMail">Mail</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	303 <option value="dijitLeaf">Leaf</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	304 <option value="dijitIconFile">File</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	305 <option value="dijitIconFunction">Function</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	306 <option value="dijitIconKey">Key</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	307 <option value="dijitIconPackage">Package</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	308 <option value="dijitIconSample">Sample</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	309 <option value="dijitIconTable">Table</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	310 <option value="dijitIconUsers">Users</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	311 <option value="dijitIconFolderClosed">Folder Closed</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	312 <option value="dijitIconFolderOpen">Folder Open</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	313 <option value="dijitIconError">Error</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	314 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	315 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	316 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	317 </xml>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	318
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	319 <xml name="menu_sanitize">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	320 <sanitizer>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	321 <valid>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	322 <add value="{"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	323 <add value="}"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	324 <add value="!"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	325 <add value="?"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	326 <add value="&"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	327 <add value="+"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	328 <add value="="/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	329 <add value="'"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	330 <add value='"'/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	331 </valid>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	332 </sanitizer>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	333 </xml>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	334
16 318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	335 <xml name="input_conditional" token_label="Track Data" token_format="data">
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	336 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
318a0aa5075a Uploaded manually iuc parents: 13 diff changeset	337 </xml>
42 c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	338 <xml name="citations">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	339 <citations>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	340 <citation type="doi">10.1101/gr.094607.109</citation>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	341 </citations>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 40 diff changeset	342 </xml>
0 c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8 iuc parents: diff changeset	343 </macros>

Mercurial > repos > iuc > jbrowse

annotate macros.xml @ 42:c1451868f8d4 draft