tools-iuc/tools/obitools/obirefidx.xml at 9bdfe69077f0cf4b35b8318c9db01835e601c2cb · galaxyproject/tools-iuc · GitHub

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<tool id="obi_refidx" name="obirefidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Index the database
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        obirefidx
        --no-progressbar
        @TAXO_DIR@
        @INPUT_FORMAT@
        @OUT_FORMAT@
        $input
        >'$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="@INPUT_FORMATS@"/>
        <expand macro="taxo_macro"/>
        <expand macro="input_format_options_macro"/>
        <expand macro="out_format_macro"/>
    </inputs>
    <outputs>
        <data format_source="input" name="output">
            <expand macro="change_format_macro"/>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="db_v05_r117.fasta.gz" ftype="fasta.gz"/>
            <conditional name="taxonomy">
                <param name="taxonomy_source" value="history"/>
                <param name="taxdump" value="taxdump_mammalia_old.csv.gz"/>
            </conditional>
            <output name="output" file="output_obirefidx_db.fasta.gz" ftype="fasta.gz"/>
        </test>
    </tests>
    <help>
        .. class:: infomark

**What it does**


@OBITOOLS_LINK_OBI4@

    </help>
    <expand macro="citation" />

</tool>