<tool id="skesa" name="skesa" version="0.1">
    <requirements>
      	<requirement type="package" version="2.2">skesa</requirement>
	<requirement type="package" >python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    

      #if $jobtype.select != "cl"
	skesa
       #if $jobtype.select == "asm"
        --fasta $draft
       #else if $jobtype.select == "se"
        --fastq $fastq1
       #else if $jobtype.select == "pe"
	--fastq $fastq1,$fastq2 --use_paired_ends
       #else if $jobtype.select == "rp"
	--fastq $jobtype.pairedf.forward,$jobtype.pairedf.reverse --use_paired_ends
       #if $cores != 0
        --cores $cores
       #end if
        --memory $memory > results.skesa.fasta
      #end if


      #if $jobtype.select == "cl"
	
	#set $pathOuput = 0
	mkdir temp_data;
        #for $collection_file in $jobtype.collection_files
             	#silent sys.stderr.write($collection_file+"\n")
	 	cp $collection_file temp_data/.;
	     
        #end for
	

      #end if

    ]]></command>
    <inputs>
      <conditional name="jobtype">
        <param name="select" type="select" label="Assembly or FASTQ Reads?">
          <option value="asm">Genome Assembly</option>
          <option value="se">Single-End Reads</option>
          <option value="pe">Paired-End Reads (Separate Files)</option>
          <option value="rp">Paired-End Reads (Paired Data Set)</option>
          <option value="cl">Collection of Reads</option>
        </param>
        <when value="srr">
          <param name="srrnum" type="text" label="Sra run number"/>
        </when>
        <when value="asm">
          <param name="draft" type="data" format="fasta" label="FASTA" />
        </when>
        <when value="se">
          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
        </when>
        <when value="pe">
          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
        </when>
        <when value="cl">
          <param name="collection_files" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
        </when>
        <when value="rp">
          <param name="pairedf" type="data_collection" collection_type="paired" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" />
        </when>
      </conditional>
      <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
      <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
    
    </inputs>
    <outputs>
            <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
    </outputs>

    <help><![CDATA[
    
**Usage: skesa**

**INPUT**

A fasta assembly or single or paired end reads test or data set list of fastqs

**Memory available**

--memory arg (=32)         Memory available (GB) [integer]
     

**Number of cores**

--cores arg (=0)           Number of cores to use (default all) [integer]

https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/

    ]]></help>
     <citations>
        <citation type="bibtex">
        @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
        title={skesa: eSKESA is a de-novo sequence read assembler for cultured single isolate genomes
    based on DeBruijn graphs. It uses conservative heuristics and is designed to
    create breaks at repeat regions in the genome. This leads to excellent sequence
    quality but not necessarily a large N50 statistic. It is a multi-threaded
    application that scales well with the number of processors. For different runs
    with the same inputs, including the order of reads, the order and orientation
    of contigs in the output is deterministic. },
        url={https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/},
        author={National Center for Biotechnology Information },
       }</citation>
    </citations>
</tool>