Mercurial > repos > fubar > jbrowse2

comparison macros.xml @ 98:b1260bca5fdc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
author bgruening
date Wed, 05 Jun 2024 10:00:07 +0000
parents 74074746ccd8
children 990291e918c7
comparison
equal deleted inserted replaced
97:74074746ccd8 98:b1260bca5fdc
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.11.0</token> 2 <token name="@TOOL_VERSION@">2.11.1</token>
3 <xml name="edamInc"> 3 <xml name="edamInc">
4 <edam_topics> 4 <edam_topics>
5 <edam_topic>topic_3307</edam_topic> 5 <edam_topic>topic_3307</edam_topic>
6 <edam_topic>topic_0092</edam_topic> 6 <edam_topic>topic_0092</edam_topic>
7 </edam_topics> 7 </edam_topics>
11 </edam_operations> 11 </edam_operations>
12 </xml> 12 </xml>
13 <xml name="requirements"> 13 <xml name="requirements">
14 <requirements> 14 <requirements>
15 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement> 15 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
16 <requirement type="package" version="1.81">biopython</requirement> 16 <requirement type="package" version="1.82">biopython</requirement>
17 <requirement type="package" version="0.7.1">bcbio-gff</requirement> 17 <requirement type="package" version="0.7.1">bcbio-gff</requirement>
18 <requirement type="package" version="1.19">samtools</requirement> 18 <requirement type="package" version="1.19">samtools</requirement>
19 <requirement type="package" version="6.0.1">pyyaml</requirement> 19 <requirement type="package" version="6.0.1">pyyaml</requirement>
20 <requirement type="package" version="1.11">tabix</requirement> 20 <requirement type="package" version="1.11">tabix</requirement>
21 <requirement type="package" version="4.6.0">findutils</requirement> 21 <requirement type="package" version="4.6.0">findutils</requirement>
23 <requirement type="package" version="3.0">zip</requirement> 23 <requirement type="package" version="3.0">zip</requirement>
24 <yield/> 24 <yield/>
25 </requirements> 25 </requirements>
26 </xml> 26 </xml>
27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> 27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
28 <token name="@WRAPPER_VERSION@">galaxy2</token> 28 <token name="@VERSION_SUFFIX@">0</token>
29 <token name="@ATTRIBUTION@"><![CDATA[
30 **Attribution**
31 This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is
32 maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own.
33 ]]>
34 </token>
35 <xml name="creators"> 29 <xml name="creators">
36 <creator> 30 <creator>
37 <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena" /> 31 <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/>
38 <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud" /> 32 <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud"/>
39 <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/" /> 33 <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/"/>
40 </creator> 34 </creator>
41 </xml> 35 </xml>
42 <xml name="genome_selector" 36 <xml name="genome_selector" token_help="" token_label="Fasta sequences" token_optional="False">
43 token_help=""
44 token_label="Fasta sequences"
45 token_optional="False" >
46 <conditional name="reference_genome"> 37 <conditional name="reference_genome">
47 <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references"> 38 <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references">
48 <option selected="True" value="indexed">Use a built-in genome</option> 39 <option selected="True" value="indexed">Use a built-in genome</option>
49 <option value="history">Use a genome from history</option> 40 <option value="history">Use a genome from history</option>
50 </param> 41 </param>
110 <option value="collect">Convert a collection of suitable track files</option> 101 <option value="collect">Convert a collection of suitable track files</option>
111 </param> 102 </param>
112 <when value="collect"> 103 <when value="collect">
113 <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/> 104 <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/>
114 </when> 105 </when>
115 <when value="form"> 106 <when value="form"/>
116 </when> 107 </conditional>
117 </conditional> 108 <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing" help="Default is to make an interactive browser appear when the 'eye' icon is activated"/>
118 <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing " help="Default is to make an interactive browser appear when the 'eye' icon is activated"/>
119 <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/> 109 <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/>
120 <param name="session_name" type="text" value="New JB2 session" label="Session name" help="Displayed at the top of the window"/> 110 <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/>
121 <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/> 111 <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/>
122 <param name="primary_color" type="color" value="#0D233F" label="Primary color"> 112 <param name="primary_color" type="color" value="#0D233F" label="Primary color">
123 <sanitizer> 113 <sanitizer>
124 <valid initial="string.ascii_letters,string.digits"> 114 <valid initial="string.ascii_letters,string.digits">
125 <add value="#"/> 115 <add value="#"/>