<tool id="spades" name="spades" version="0.7">
  <description>SPAdes genome assembler for regular and single-cell projects</description>
  <requirements>
    <requirement type="package" version="2.5.1">spades</requirement>
  </requirements>
  <command interpreter="perl">spades.pl 
     $out_contigs 
     $out_contig_stats 
     $out_scaffolds 
     $out_scaffold_stats 
     $out_log 
    ## 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
    ## Forces unzipped output, faster
    --disable-gzip-output
    $sc
    $onlyassembler
    $careful
    ##$rectangles
    -t \${GALAXY_SLOTS:-16}
    -k "$kmers"
    ##-i $iterations 
    ##--phred-offset
    ## Sequence files
    #for $i, $library in enumerate( $libraries )
      #set num=$i+1
      #if str( $library.lib_type ) == "paired_end":
        #set prefix = 'pe'
      #else:
        #set prefix = 'mp'
      #end if
      --$prefix$num-$library.orientation    
      #for $file in $library.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 $file.file_type.type == "unpaired"
          --$prefix$num-s fastq:$file.file_type.unpaired_reads
        #end if
      #end for
    #end for
  </command>
  <inputs>
    <param name="sc" type="boolean" truevalue="--sc" falsevalue="" label="Single-cell?" help="This option is required for MDA (single-cell) data.">
      <option value="false">No</option>
      <option value="true">Yes</option>
    </param>
    <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
    <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." />
    <!-- <param name="rectangles" type="boolean" truevalue="- -rectangles" falsevalue="" checked="False" label="Use rectangle graph algorithm for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental, use at your own risks)." /> It uses a different format for the sequence identifier in the output FASTA files which do not contain the coverage information -->
    <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1" /> -->
    <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." >
    </param>
    <!-- Reads -->
    <repeat name="libraries" title="Libraries" min="1" 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.">
      <param name="lib_type" type="select" label="Library type">
	<option value="paired_end">Paired-end / Single reads</option>
	<option value="mate_paired">Mate pairs</option>
      </param>
      <param name="orientation" type="select" label="Orientation">
	<option value="fr" selected="true">-> &lt;- (fr)</option>
	<option value="rf">&lt;- -> (rf)</option>
	<option value="ff">-> -> (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="unpaired">Unpaired/Single reads</option>
	  </param>
	  <when value="separate">
	    <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
	    <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
	  </when>
	  <when value="interleaved">
	    <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
	  </when>
	  <when value="unpaired">
	    <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" />
	  </when>
	</conditional>
      </repeat>
    </repeat>
  </inputs>
  <outputs>
    <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
    <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" />
    <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
    <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
    <data name="out_log" format="txt" label="SPAdes log" />
  </outputs>
  <!--  <tests>
    <test>
      <param name="sc" value="false" />
      <param name="careful" value="false" />
      <param name="kmers" value="33,55" />
      <param name="type" value="pairedend" />
      <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>
  </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 2.5.1, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. 

**SPAdes citation**

Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021. 
  
**License**

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

This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

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 bugs in the 0.6 version.
  </help>
</tool>