view macros.xml @ 0:7c6c282ecf5a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac

<macros>
    <token name="@VERSION@">0.7</token>
    <token name="@PROFILE@">21.05</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">cherri</requirement>
        </requirements>
    </xml>
    <macro name="reference_source_conditional">
        <conditional name="ref_source">
            <param name="ref_source_selector" type="select" label="Reference genome in FASTA format">
                <option value="cached">locally cached</option>
                <option value="history">in your history</option>
            </param>
            <when value="cached">
                <param name="genome_fasta" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No indices are available." />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="genome_fasta" type="data" format="fasta" label="Select a reference dataset in FASTA format" />
            </when>
        </conditional>
        <param name="chrom_len_file" type="data" format="tabular" label="Two column tabular file containing chromosome lengths" help="Format: 'chrom name' \t 'chrom length'" />        
    </macro>
    <token name="@COMMONPARAMS@" ><![CDATA[
            #if $intarna_param_file: 
                -p '$intarna_param_file'
            #end if
            -c '$context'
            -st $use_structure
            -t '$run_time'
            -me "\${GALAXY_MEMORY_MB_PER_SLOT:-8000}"
            -j "\${GALAXY_SLOTS:-1}"
        ]]></token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0080</edam_topic>
            <edam_topic>topic_0081</edam_topic>
            <edam_topic>topic_0160</edam_topic>
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_2995</edam_operation>
        </edam_operations>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">cherri</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">cherri</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <yield />
        </citations>
    </xml>
</macros>