annotate macros.xml @ 0:465d6578b4d0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8

<macros>
    <token name="@TOOL_VERSION@">2.3.8</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">circexplorer2</requirement>
        </requirements>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">circexplorer2</xref>
        </xrefs>
    </xml>
    <xml name="parse_fusion" token_format="" token_label="" token_help="">
        <param name="fusion_file" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP@"/>
    </xml>
    <xml name="parse_statistics">
        <param argument="-f" type="boolean" truevalue="-f" falsevalue="" checked="false" 
            label="Statistics fragment numbers rather than read numbers"/>
    </xml>
    <xml name="genome_file">
        <param argument="--genome" type="data" format="fasta" label="Reference genome" help="In FASTA format"/>
    </xml>
    <xml name="annotation_file">
        <param argument="--ref" type="data" format="txt" label="Gene annotation" 
            help="The file is in the format of Gene Predictions and RefSeq Genes with Gene Names" />
    </xml>
    <xml name="junction_file">
        <param argument="--bed" type="data" format="bed" label="Back spliced junction file" 
            help="This file can be created by CIRCexplorer2 parse or CIRCexplorer2 align" />
    </xml>
    <xml name="tophat_file">
        <param argument="--tophat" type="data" format="tgz" label="TopHat alignment file" 
        help="Generated by the align module" />
    </xml>
    <token name="@threads@"><![CDATA[--thread=\${GALAXY_SLOTS:-10}]]></token> 
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.202895.115</citation>
        </citations>
    </xml>
</macros>