jbrowse: macros.xml annotate

annotate macros.xml @ 6:ecbdfc775b9a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98

author	iuc
date	Sat, 25 Jun 2016 16:44:39 -0400
parents	ae9382cfb6ac
children	ad4b9d7eae6a

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>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	5 <requirement type="package" version="1.12.0">jbrowse</requirement>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	6 <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	7 <requirement type="package" version="2.7">python</requirement>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	8 <requirement type="package" version="5.18.1">perl</requirement>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	9 <requirement type="package" version="1.66">biopython</requirement>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	10 <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	11 <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	12 <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	13 <yield/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	14 </requirements>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	15 </xml>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	16 <token name="@WRAPPER_VERSION@">1.0</token>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	17 <xml name="stdio">
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	18 <stdio>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	19 <exit_code range="1:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	20 <exit_code range=":-1"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	21 <regex match="Error:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	22 <regex match="Exception:"/>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	23 </stdio>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	24 </xml>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	25 <token name="@ATTRIBUTION@"><![CDATA[
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	26 Attribution
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	27
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	28 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	29 ]]>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	30 </token>
6 ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	31
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	32 <xml name="genome_selector"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	33 token_help=""
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	34 token_label="Fasta sequences"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	35 token_optional="False" >
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	36 <conditional name="reference_genome">
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	37 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	38 <option selected="True" value="indexed">Use a built-in genome</option>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	39 <option value="history">Use a genome from history</option>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	40 </param>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	41 <when value="indexed">
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	42 <param
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	43 help="@HELP@"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	44 label="@LABEL@"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	45 name="genomes"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	46 type="select"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	47 optional="@OPTIONAL@"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	48 >
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	49 <options from_data_table="all_fasta">
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	50 <filter column="2" type="sort_by" />
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	51 <validator message="No genomes are available for the selected input dataset" type="no_options" />
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	52 </options>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	53 </param>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	54 </when>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	55 <when value="history">
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	56 <param
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	57 format="fasta"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	58 label="@LABEL@"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	59 help="@HELP@"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	60 name="genomes"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	61 type="data"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	62 optional="@OPTIONAL@"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	63 multiple="True" />
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	64 </when>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	65 </conditional>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	66 </xml>
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	67
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	68 <xml name="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	69 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	70 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	71 token_select_label="Color Specification"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	72 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	73 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	74 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	75 <conditional name="@COND_NAME@" label="@COND_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	76 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	77 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	78 <option value="manual">@MANUAL_LABEL@</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	79 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	80 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	81 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	82 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	83 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	84 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	85 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	86 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	87
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	88 <xml name="track_display">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	89 <param type="select" label="Track Visibility" name="track_visibility">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	90 <option value="default_off">Off for new users</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	91 <option value="default_on">On for new users</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	92 <option value="force">Force On</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	93 <option value="always">Always On (ignores URL parameters)</option>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	94 </param>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	95 </xml>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	96
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	97 <xml name="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	98 token_label="JBrowse style.color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	99 token_name="style_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	100 token_value="goldenrod"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	101 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	102 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	103 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	104 <sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	105 <valid initial="string.letters,string.digits">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	106 <add value="#" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	107 </valid>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	108 </sanitizer>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	109 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	110 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	111
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	112 <xml name="auto_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	113 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	114 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	115 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	116 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	117 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	118 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	119 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	120 cond_label="@COND_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	121 cond_name="@COND_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	122 select_label="@SELECT_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	123 select_name="@SELECT_NAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	124 automatic_label="@AUTOMATIC_LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	125 manual_label="@MANUAL_LABEL@">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	126 <expand macro="jb_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	127 <yield />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	128 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	129 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	130
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	131
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	132
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	133 <xml name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	134 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	135 <option value="BrBg">BrBg: Brown - Blue Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	136 <option value="PiYg">PiYg: Pink - Yellow Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	137 <option value="PRGn">PRGn: Purple Red - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	138 <option value="PuOr">PuOr: Purple - Orange</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	139 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	140 <option value="RdGy">RdGy: Red - Gray</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	141 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	142 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	143 <option value="Spectral">Spectral</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	144 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	145 </xml>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	146 <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	147 <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	148 <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	149 <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	150
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	151 <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	152 <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	153
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	154 <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	155 <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	156 <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	157 <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	158
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	159 <param label="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	160 </section>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	161 </xml>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	162 <xml name="color_selection_minmax">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	163 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	164 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	165 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	166 red/blue" -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	167 <expand macro="auto_manual_tk"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	168 token_cond_label="Color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	169 token_cond_name="color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	170 token_select_label="Color Selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	171 token_select_name="color_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	172 token_automatic_label="Automatically selected"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	173 token_manual_label="Manual Color Selection">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	174 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	175 label="JBrowse style.pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	176 name="style_pos_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	177 value="blue"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	178 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	179 <expand macro="jb_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	180 label="JBrowse style.neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	181 name="style_neg_color"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	182 value="red"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	183 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	184 </expand>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	185
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	186 <conditional name="bicolor_pivot" label="Bicolor Pivot">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	187 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	188 <option value="zero" selected="true">Zero</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	189 <option value="mean">Mean</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	190 <option value="custom">Custom Value</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	191 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	192 <when value="zero" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	193 <when value="mean" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	194 <when value="custom">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	195 <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	196 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	197 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	198 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	199 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	200
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	201 <xml name="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	202 token_scaling_lin_select="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	203 token_scaling_log_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	204 >
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	205 <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	206 <conditional name="color_score" label="JBrowse style.color & Score relationship">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	207 <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	208 <option value="score">Based on score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	209 <option value="none" selected="true">Ignore score</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	210 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	211 <when value="none">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	212 <!-- When no scaling is done, no scores available, then just let the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	213 user choose a base color for the track -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	214 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	215 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	216 <when value="score">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	217 <!-- Scaling -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	218 <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	219 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	220 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	221 <option value="logarithmic" selected="" >Logarithmic scaling</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	222 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	223 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	224
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	225 <!-- Scaling Bounds -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	226 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	227 <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	228 <option value="automatic" selected="true">Automatically determined</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	229 <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	230 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	231 <when value="automatic">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	232 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	233 <when value="manual">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	234 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	235 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	236 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	237 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	238
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	239 <!-- Scale color -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	240 <conditional name="color_scheme" label="Color Scheme for scored features">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	241 <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	242 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	243 <!--<option value="brewer">Brewer Color Schemes</option>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	244 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	245 <when value="opacity">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	246 <!-- Single color selection mode -->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	247 <expand macro="auto_color" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	248 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	249 <!--<when value="brewer">-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	250 <!--[> Brewer continuum selection <]-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	251 <!--<expand macro="brewer_scheme" />-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	252 <!--</when>-->
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	253 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	254 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	255 </conditional>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	256 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	257 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	258 <xml name="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	259 token_classname="feature"
6 ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	260 token_label="prodcut,name,id"
ecbdfc775b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98 iuc parents: 5 diff changeset	261 token_description="note"
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	262 token_height="100px">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	263 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	264 <param label="JBrowse style.className" type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	265 name="style_classname"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	266 value="@CLASSNAME@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	267 help="Set CSS style.className property"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	268 <param label="JBrowse style.label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	269 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	270 name="style_label"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	271 value="@LABEL@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	272 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	273 <param label="JBrowse style.description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	274 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	275 name="style_description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	276 value="@DESCRIPTION@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	277 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	278 <param label="JBrowse style.height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	279 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	280 name="style_height"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	281 value="@HEIGHT@"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	282 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	283 </section>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	284 </xml>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	285
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	286 <xml name="input_conditional" token_label="Track Data" token_format="data">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	287 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 2 diff changeset	288 </xml>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	289 </macros>

Mercurial > repos > iuc > jbrowse

annotate macros.xml @ 6:ecbdfc775b9a draft