<tool id="megan_daa2rma" name="MEGAN: Generate a MEGAN rma6 file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>from a DIAMOND daa file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#set input_identifier = 'input.' + $in.ext
ln -s '${in}' '${input_identifier}' &&

daa2rma
--in '${input_identifier}'
#if $advanced_options.metaDataFile:
    --metaDataFile '$advanced_options.metaDataFile'
#end if
#if str($advanced_options.paired_reads_cond.paired_reads) == 'yes':
    --paired
    $advanced_options.paired_reads_cond.pairedSuffixLength
#end if
$advanced_options.longReads
--maxMatchesPerRead $advanced_options.maxMatchesPerRead
$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
--out '$output'
--threads \${GALAXY_SLOTS:-8}
--tempStoreDir '.'
    ]]></command>
    <inputs>
        <expand macro="input_daa_param"/>
        <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"/>
            <conditional name="paired_reads_cond">
                <param name="paired_reads" type="select" label="DAA file was created using paired reads?">
                    <option value="no" selected="true">no</option>
                    <option value="yes">Yes</option>
                </param>
                <when value="no"/>
                <when value="yes">
                    <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
                </when>
            </conditional>
            <expand macro="long_reads_param"/>
            <expand macro="max_matches_per_read_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"/>
            <expand macro="only_named_classifications_param"/>
        </section>
    </inputs>
    <outputs>
        <data name="output" format="rma6"/>
    </outputs>
    <tests>
        <test>
            <param name="in" ftype="daa" value="input.daa"/>
            <output name="output" ftype="rma6">
                <assert_contents>
                    <has_size value="1487"/>
                </assert_contents>
            </output>
       </test>
        <test>
            <param name="in" ftype="daa" value="input.daa"/>
            <param name="longReads" value="true"/>
            <param name="minScore" value="25.0"/>
            <param name="maxExpected" value="0.05"/>
            <param name="lcaAlgorithm" value="weighted"/>
            <output name="output" ftype="rma6">
                <assert_contents>
                    <has_size value="1445"/>
                </assert_contents>
            </output>
       </test>
    </tests>
    <help>
**What it does**

Computes a MEGAN RMA (RealMedia Audio) file from a DIOMAND DAA file, a proprietary file format developed by PowerISO Computing
for disk image files.  MEGAN uses an update of the original RMA file format known as RMA6.
    </help>
    <expand macro="citations"/>
</tool>