comparison macros.xml @ 98:b1260bca5fdc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6

97:74074746ccd8

<macros>
    <token name="@TOOL_VERSION@">2.11.0</token>
    <xml name="edamInc">
        <edam_topics>
            <edam_topic>topic_3307</edam_topic>
            <edam_topic>topic_0092</edam_topic>
        </edam_topics>

        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
            <requirement type="package" version="1.81">biopython</requirement>
            <requirement type="package" version="0.7.1">bcbio-gff</requirement>
            <requirement type="package" version="1.19">samtools</requirement>
            <requirement type="package" version="6.0.1">pyyaml</requirement>
            <requirement type="package" version="1.11">tabix</requirement>
            <requirement type="package" version="4.6.0">findutils</requirement>

            <requirement type="package" version="3.0">zip</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
    <token name="@WRAPPER_VERSION@">galaxy2</token>
    <token name="@ATTRIBUTION@"><![CDATA[
**Attribution**
This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is 
maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own.
]]>
    </token>
    <xml name="creators">
        <creator>
            <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena" />
            <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud" />
            <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/" />
        </creator>
    </xml>
    <xml name="genome_selector"
        token_help=""
        token_label="Fasta sequences"
        token_optional="False" >
        <conditional name="reference_genome">
            <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references">
                <option selected="True" value="indexed">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>
            </param>

                    <option value="collect">Convert a collection of suitable track files</option>
                </param>
                <when value="collect">
                    <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/>
                </when>
                <when value="form">
                </when>
            </conditional>
            <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"/>
            <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"/>
            <param name="session_name" type="text" value="New JB2 session" label="Session name" help="Displayed at the top of the window"/>
            <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"/>
            <param name="primary_color" type="color" value="#0D233F" label="Primary color">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>

98:b1260bca5fdc

<macros>
    <token name="@TOOL_VERSION@">2.11.1</token>
    <xml name="edamInc">
        <edam_topics>
            <edam_topic>topic_3307</edam_topic>
            <edam_topic>topic_0092</edam_topic>
        </edam_topics>

        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
            <requirement type="package" version="1.82">biopython</requirement>
            <requirement type="package" version="0.7.1">bcbio-gff</requirement>
            <requirement type="package" version="1.19">samtools</requirement>
            <requirement type="package" version="6.0.1">pyyaml</requirement>
            <requirement type="package" version="1.11">tabix</requirement>
            <requirement type="package" version="4.6.0">findutils</requirement>

            <requirement type="package" version="3.0">zip</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="creators">
        <creator>
            <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/>
            <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud"/>
            <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/"/>
        </creator>
    </xml>
    <xml name="genome_selector" token_help="" token_label="Fasta sequences" token_optional="False">
        <conditional name="reference_genome">
            <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references">
                <option selected="True" value="indexed">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>
            </param>

                    <option value="collect">Convert a collection of suitable track files</option>
                </param>
                <when value="collect">
                    <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/>
                </when>
                <when value="form"/>
            </conditional>
            <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"/>
            <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"/>
            <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/>
            <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"/>
            <param name="primary_color" type="color" value="#0D233F" label="Primary color">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>