<?xml version='1.0' encoding='utf-8'?>
<tool id="megahit" name="MEGAHIT" version="1.1.2.1">
    <description>metagenomics assembly</description>
    <requirements>
        <requirement type="package" version="1.1.2">megahit</requirement>
    </requirements>
    <version_command>megahit --version</version_command>
    <command detect_errors="exit_code"><![CDATA[

    megahit

    #if $input_option.choice == 'paired'
        -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.fastq_input1]) }
        -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) }
    #else
        -r '${input_option.single_files}'
    #end if

    ##basic assembly
    --min-count '${basic_section.min_count}'
    --k-min '${basic_section.k_min}'
    --k-max '${basic_section.k_max}'
    --k-step '${basic_section.k_step}'
    --min-contig-len '${basic_section.min_contig_len}'

    ##advanced assembly
    ${advanced_section.nomercy}
    --bubble-level '${advanced_section.bubble_level}'
    --merge-level '${advanced_section.merge_level}'
    --prune-level '${advanced_section.prune_level}'
    --prune-depth '${advanced_section.prune_depth}'
    --low-local-ratio '${advanced_section.low_local_ratio}'
    ${advanced_section.nolocal}
    ${advanced_section.kmin1pass}

    &&

    cat megahit_out/log

    ]]></command>

    <inputs>
        <conditional name="input_option">
            <param name="choice" type="select" label="Select your input option">
                <option value="single" selected="true">Single</option>
                <option value="paired">Paired-end</option>
            </param>
            <when value="paired">
                <param name="fastq_input1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="list:paired" label="Select a paired collection"/>
            </when>
            <when value="single">
                <param name="single_files" multiple="true" format="fastq,fastqsanger,fasta" type="data" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" />
            </when>
        </conditional>
        <section name="basic_section" title="Basic assembly options" expanded="True">
            <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
            <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
            <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="255" help="must be odd number"/>
            <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
            <param name="k_step" argument="--k-step" type="integer" value="12" label="increment of kmer size of each iteration" max="28" help="must be even number"/>
        </section>
        <section name="advanced_section" title="Advanced assembly options" expanded="False">
            <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue=""  label="do not add mercy kmers" />
            <param name="bubble_level" argument="--bubble-level" type="integer" value="2" min="0" max="2" label="intensity of bubble merging (0-2), 0 to disable" />
            <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" />
            <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />
            <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="remove unitigs with avg kmer depth less than this value" />
            <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" />
            <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
            <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" />
        </section>
    </inputs>
    <outputs>
        <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <conditional name="input_option">
                <param name="choice" value="single"/>
                <param name="single_files" value="refExample.fa" ftype="fasta"/>
            </conditional>
            <output name="output" file="single_result.fa"/>
        </test>
        <test>
            <conditional name="input_option">
                <param name="choice" value="paired"/>
                <param name="fastq_input1">
                    <collection type="list:paired">
                        <element name="Pair1">
                            <collection type="paired">
                                <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
                                <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
                            </collection>
                        </element>
                    </collection>
                </param>
            </conditional>
            <output name="output" file="paired_result.fa"/>
        </test>
    </tests>

    <help><![CDATA[

**What it does**

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5.

--------

**Project links:**

https://github.com/voutcn/megahit


    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btv033</citation>
    </citations>
</tool>