<tool id="rnaspades" name="rnaSPAdes" version="3.9.0.1">
    <description>assembler for RNA-Seq data</description>
    <requirements>
        <requirement type="package" version="3.9.0">spades</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        <![CDATA[
        rnaspades.py -o .
        ## Forces unzipped output, faster
        --disable-gzip-output
        $draft $onlyassembler -t \${GALAXY_SLOTS:-4} $iontorrent -k $kmer
        ## Sequence files, libraries
        #for $i, $library in enumerate( $libraries, start=1 ):
            #if str( $library.lib_type ) == "paired_end":
                #set prefix = 'pe'
            #elif str( $library.lib_type ) == "mate_paired":
                #set prefix = 'mp'
            #elif str( $library.lib_type ) == "nxmate_paired":
                #set prefix = 'nxmate'
            #else:
                #set prefix = 'hqmp'
            #end if
            --$prefix$i-$library.orientation
            #for $file in $library.files
                #if $file.file_type.type == "separate":
                    --$prefix$i-1 fastq:$file.file_type.fwd_reads
                    --$prefix$i-2 fastq:$file.file_type.rev_reads
                #elif $file.file_type.type == "interleaved":
                    --$prefix$i-12 fastq:$file.file_type.interleaved_reads
                #elif $file.file_type.type == "unpaired":
                    --$prefix$i-s fastq:$file.file_type.unpaired_reads
                #elif $file.file_type.type == "paired-collection":
                    --$prefix$i-1 fastq:$file.file_type.fastq_collection.forward
                    --$prefix$i-2 fastq:$file.file_type.fastq_collection.reverse
                #end if
            #end for
        #end for
        #for $contig in $trusted_contigs:
            #if $contig:
                --trusted-contigs $contig.extension:$contig
            #end if
        #end for
        #for $contig in $untrusted_contigs:
            #if $contig:
                --untrusted-contigs $contig.extension:$contig
            #end if
        #end for
        ]]>
    </command>
    <inputs>
        <param argument="--draft-assembly" checked="False" falsevalue="" label="Draft assembly. Faster, but more error-prone" name="draft" truevalue="--draft-assembly" type="boolean" />
        <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
        <param argument="--iontorrent" checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
        <param argument="-k" max="127" label="k-mer size (must be odd and less than 128)" name="kmer" type="integer" value="55" />
        <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" name="libraries" title="Libraries">
            <param label="Library type" name="lib_type" type="select">
                <option value="paired_end">Paired-end / Single reads</option>
                <option value="mate_paired">Mate pairs</option>
                <option value="high_mate_paired">High Quality Mate pairs</option>
                <option value="nxmate_paired">Lucigen NxMate pairs</option>
            </param>
            <param label="Orientation" name="orientation" type="select">
                <option selected="true" value="fr">-&gt; &lt;- (fr)</option>
                <option value="rf"><![CDATA[<- -> (rf)]]></option>
                <option value="ff"><![CDATA[-> -> (ff)]]></option>
            </param>
            <repeat min="1" name="files" title="Files">
                <conditional name="file_type">
                    <param label="Select file format" name="type" type="select">
                        <option value="separate">Separate input files</option>
                        <option value="interleaved">Interleaved files</option>
                        <option value="unpaired">Unpaired/Single reads</option>
                        <option value="paired-collection">Paired List Collection</option>
                    </param>
                    <when value="separate">
                        <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
                        <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
                    </when>
                    <when value="interleaved">
                        <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
                    </when>
                    <when value="unpaired">
                        <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
                    </when>
                    <when value="paired-collection">
                        <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
                    </when>
                </conditional>
            </repeat>
        </repeat>
        <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
        <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
    </inputs>
    <outputs>
        <data format="fasta" label="rnaSPAdes transcripts" name="output_transcripts" from_work_dir="transcripts.fasta" />
    </outputs>
    <tests>
        <test>
            <param name="lib_type" value="paired_end" />
            <param name="type" value="separate" />
            <param name="fwd_reads" value="rnaspades-in1-1.fq" ftype="fastq" />
            <param name="rev_reads" value="rnaspades-in1-2.fq" ftype="fastq" />
            <output name="output_transcripts" file="rnaspades-out1.fa" ftype="fasta" compare="re_match" lines_diff="1" />
        </test>
    </tests>
    <help>
**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.

This wrapper runs SPAdes 3.9.0, collects the output, and throws away all the temporary files.

**License**

SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.

The original wrapper was written by Lionel Guy, Philip Mabon and was released under the GNU General Public License as published by the Free Software Foundation. The rnaSPAdes extension was developed by the Galaxy team.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.

** Acknowledgments **

Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.

Nicola Soranzo fixed various bugs.
    </help>
    <citations>
        <citation type="doi">10.1089/cmb.2012.0021</citation>
    </citations>
</tool>