<tool id="metaspades" name="metaSPAdes" version="3.9.0.1">
    <description>assembler for metagenomics datasets</description>
    <requirements>
        <requirement type="package" version="3.9.0">spades</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
    <![CDATA[

    if [[ -n \$GALAXY_MEMORY_MB ]]; then
        GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
    fi &&

    ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
    spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
    #if not $kmer_choice.auto_kmer_choice:
        -k "$kmer_choice.kmers"
    #end if
    ## Sequence files
    #set num=1
    #if str( $lib_type ) == "paired_end":
        #set prefix = 'pe'
    #end if
    --$prefix$num-$orientation
    #for $file in $files
        #if $file.file_type.type == "separate"
            --$prefix$num-1 fastq:$file.file_type.fwd_reads
            --$prefix$num-2 fastq:$file.file_type.rev_reads
        #elif $file.file_type.type == "interleaved"
            --$prefix$num-12 fastq:$file.file_type.interleaved_reads
        #elif $file.file_type.type == "paired-collection"
            --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
            --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
        #end if
    #end for
    ]]>
    </command>
    <inputs>
        <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
        <conditional name="kmer_choice">
            <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" />
            <when value="false">
                <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." />
            </when>
            <when value="true" />
        </conditional>
        <param name="lib_type" type="select" label="Library type">
            <option value="paired_end">Paired-end</option>
        </param>
        <param label="Orientation" name="orientation" type="select">
            <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
            <option value="rf"><![CDATA[<- -> (rf)]]></option>
            <option value="ff"><![CDATA[-> -> (ff)]]></option>
        </param>
        <repeat name="files" title="Files" min="1">
            <conditional name="file_type">
                <param name="type" type="select" label="Select file format">
                    <option value="separate">Separate input files</option>
                    <option value="interleaved">Interleaved files</option>
                    <option value="paired-collection">Paired List Collection</option>
                </param>
                <when value="separate">
                    <param name="fwd_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="FASTQ format" />
                    <param name="rev_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="FASTQ format" />
                </when>
                <when value="interleaved">
                    <param name="interleaved_reads" type="data" format="fastq,fastq.gz" label="Interleaved paired reads" help="FASTQ format" />
                </when>
                <when value="paired-collection">
                    <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq,fastq.gz" collection_type="paired" help="FASTQ format" />
                </when>
            </conditional>
        </repeat>
    </inputs>
    <outputs>
        <data name="out_contigs" format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" />
        <data name="out_scaffolds" format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" />
        <data name="out_fastg" format="txt" from_work_dir="assembly_graph.fastg" label="SPAdes assembly graph (fastg)" />
        <data name="out_log" format="txt" from_work_dir="spades.log" label="SPAdes log" />
    </outputs>
    <tests>
        <test>
            <param name="sc" value="false" />
            <param name="careful" value="false" />
            <param name="kmers" value="33,55" />
            <param name="lib_type" value="paired_end" />
            <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
            <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
            <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
        </test>
        <test>
            <param name="sc" value="false" />
            <param name="careful" value="false" />
            <param name="kmers" value="33,55" />
            <param name="lib_type" value="paired_end" />
            <param name="fwd_reads" value="ecoli_1K_1.fq.gz" ftype="fastq.gz" />
            <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" />
            <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
]]>
    </help>
    <citations>
        <citation type="doi">10.1089/cmb.2012.0021</citation>
    </citations>
</tool>