<tool id="megan_daa_meganizer" name="MEGAN: meganize a DIAMOND file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>for use with MEGAN</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
## daa-meganizer "meganizes" the input, altering
## the file itself instead of producing a separate
## output.  We'll make a copy of the input to handle
## this issue.  The input must also have a .daa file
## extension.
#set input_identifier = 'input.' + $in.ext
cp '${in}' '${input_identifier}' &&

daa-meganizer
--in '${input_identifier}'
#if $advanced_options.metaDataFile:
    --metaDataFile '$advanced_options.metaDataFile'
#end if
$advanced_options.longReads
$advanced_options.classify
--minScore $advanced_options.minScore
--maxExpected $advanced_options.maxExpected
--minPercentIdentity $advanced_options.minPercentIdentity
--topPercent $advanced_options.topPercent
--minSupportPercent $advanced_options.minSupportPercent
--minSupport $advanced_options.minSupport
--minPercentReadCover $advanced_options.minPercentReadCover
--minPercentReferenceCover $advanced_options.minPercentReferenceCover
--minReadLength $advanced_options.minReadLength
--lcaAlgorithm '$advanced_options.lcaAlgorithm'
--lcaCoveragePercent $advanced_options.lcaCoveragePercent
--readAssignmentMode '$advanced_options.readAssignmentMode'
#if $advanced_options.conFile:
    --conFile '$advanced_options.conFile'
#end if
#if $advanced_options.mapDB:
    --mapDB '$advanced_options.mapDB'
#end if
#if str($advanced_options.only) != '':
    --only '$advanced_options.only'
#end if
--threads \${GALAXY_SLOTS:-8}
--tempStoreDir '.'
&& mv '$input_identifier' '$output'
    ]]></command>
    <inputs>
        <param argument="--in" type="data" format="daa" label="Input DAA file"/>
        <section name="advanced_options" title="Advanced options" expanded="false">
            <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
            <expand macro="long_reads_param"/>
            <expand macro="classify_param"/>
            <expand macro="blast_params"/>
            <expand macro="min_max_params"/>
            <expand macro="lca_params"/>
            <expand macro="read_assignment_mode_param"/>
            <expand macro="con_file_param"/>
            <expand macro="mapdb_param"/>
            <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
                <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="output" format="daa"/>
    </outputs>
    <tests>
        <test>
            <param name="in" ftype="daa" value="input.daa"/>
            <output name="output" ftype="daa">
                <assert_contents>
                    <has_size value="3500"/>
                </assert_contents>
            </output>
       </test>
    </tests>
    <help>
**What it does**

Meganizes a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
for disk image files.  The output is a DIAMOND file consisting of the original input file, but with additional blocks of
information appended to the end of the file.

    </help>
    <expand macro="citations"/>
</tool>