<tool id="microrunqc" name="microrunqc" version="1.0.0">

  <requirements>
    <requirement type="package">skesa</requirement>
    <requirement type="package">mlst</requirement>
    <requirement type="package">bwa</requirement>
    <requirement type="package">numpy</requirement>
    <requirement type="package">fastq-scan</requirement>
  </requirements>

  <command detect_errors="exit_code"><![CDATA[

    skesa

    #set fqscan = "text"
    #if $jobtype.select == "fastq_fr"
      #set outname = $jobtype.fastq1.name
      #set bwalist = str($jobtype.fastq1) + " " + str($jobtype.fastq2)
      --fastq $jobtype.fastq1,$jobtype.fastq2
      #if $jobtype.fastq1.is_of_type("fastq.gz")
        #set fqscan = "gz"
      #else if $jobtype.fastq1.is_of_type("fastqsanger.gz")
        #set fqscan = "gz"
      #end if
    #else if $jobtype.select == "fastq_pair"
      #set outname = $jobtype.coll.name
      #set bwalist = str($jobtype.coll.forward) + " " + str($jobtype.coll.reverse)
      --fastq $jobtype.coll.forward,$jobtype.coll.reverse
      #if $jobtype.coll.forward.is_of_type("fastq.gz")
        #set fqscan = "gz"
      #else if $jobtype.coll.forward.is_of_type("fastqsanger.gz")
        #set fqscan = "gz"
      #end if
    #end if

    #set num_cores = 1

    #if $options.select =="basic"
      --cores $num_cores 
      --memory 8 
    #else if $options.select=="advanced"
      #if $options.cores
        #set num_cores = $options.cores
        --cores $options.cores
      #end if
      #if $options.memory
        --memory $options.memory
      #end if
      #if $options.hash_count
        --hash_count
      #end if
      #if $options.estimated_kmers
        --estimated_kmers $options.estimated.kmers
      #end if
      #if $options.skip
       --skip_bloom_filter
      #end if
      #if $options.kmer
       --kmer $options.kmer 
      #end if
      #if $options.min_count
       --min_count $options.min_count 
      #end if
      #if $options.max_kmer_count
       --max_kmer_count $options.max_kmer_count 
      #end if
      #if $options.vector_percent
       --vector_percent $options.vector_percent 
      #end if
      #if $options.insert_size
       --insert_size $options.insert.size 
      #end if
      #if $options.steps
       --steps $options.steps 
      #end if
      #if $options.fraction
       --fraction $options.fraction 
      #end if
      #if $options.max_snp_len
       --max_snp_len $options.max_snp_len 
      #end if
      #if $options.min_contig
       --min_contig $options.min_contig 
      #end if
      #if $options.allow_snps
       --allow_snps 
      #end if
    #end if

    > ${outname}.fasta; 

    bwa index ${outname}.fasta;
    bwa mem -t $num_cores  ${outname}.fasta ${bwalist} | python $__tool_directory__/median_size.py > insert.median;
 
    mlst --nopath --threads $num_cores 
    #if $options.select=="advanced"
      #if $options.minid
        --minid $options.minid
      #end if
      #if $options.mincov
        --mincov $options.mincov
      #end if
      #if $options.minscore
        --minscore $options.minscore
      #end if
    #end if
    ${outname}.fasta > ${outname}.mlst.tsv;

    python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan};

    python $__tool_directory__/sum_mlst.py --fasta ${outname}.fasta --mlst ${outname}.mlst.tsv --med insert.median --fqscan fq_out.tab --out sum_qc.txt 

  ]]></command>
    <inputs>
      <conditional name="jobtype">
        <param name="select" type="select" label="Select Input">
          <option value="fastq_fr">Forward and Reverse FASTQ</option>
          <option value="fastq_pair">Paired FASTQ Collection</option>
        </param>
        <when value="fastq_fr">
          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Forward FASTQ" />
          <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Reverse FASTQ" />
        </when>
        <when value="fastq_pair">
          <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
        </when>
      </conditional>
  
      <conditional name="options">
        <param name="select" type="select" label="Options Type">
          <option value="basic">Basic</option>
          <option value="advanced">Advanced</option>
        </param>
        <when value="advanced">
          <param name="cores" optional="true" type="integer" label="Number of cores to use (Default=16)" value=""/>
          <param name="memory" optional="true" type="integer" label="Memory available (Default=32GB)" value=""/>
          <param name="hash_count" optional="true" type="boolean" label="hash counter"/>
          <param name="estimated_kmers" optional="true" type="integer" label="Estimated number of unique kmers for bloom filter (Default=100)" value=""/>
          <param name="skip" optional="true" type="boolean" label="skip bloom filter, use estimate kmers as the hash"/>
          <param name="kmer" optional="true" type="integer" label="Minimal kmer length for assembly (Default=21)" value=""/>
          <param name="min_count" optional="true" type="integer" label="Minimal count for kmers retained for comparing alternate choices" value=""/>
          <param name="max_kmer_count" optional="true" type="integer" label="Minimum acceptable average count for estimating the maximal kmer length in reads" value=""/>
          <param name="vector_percent" optional="true" type="float" label="Count for vectors as a fraction of the read number (0-1,1=disabled)"  value="">
            <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
          </param>
          <param name="insert_size" optional="true" type="integer" label="Expected insert size for paired reads" value=""/>
          <param name="steps" optional="true" type="integer" label="Number of assembly iterations from minimal to maximal kmer length in reads (Default=11)" value=""/>
          <param name="fraction" optional="true" type="float" label="Maximum noise to signal ratio acceptable for extension (Default=0.1)" value="">
            <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
          </param>
          <param name="max_snp_len" optional="true" type="integer" label="Maximal snp length (Default=150)" value=""/>
          <param name="min_contig" optional="true" type="integer" label="Minimal contig length reported in output (Default=200)" value=""/>
          <param name="allow_snps" optional="true" type="boolean" label="Turn SNP discovery (Default=false)"/>
          <param name="mincov" type="integer" label="Minimum DNA %coverage" value="10" help="Minimum DNA %coverage to report partial allele at all (default 10, must be between 0-100)" optional="true" />
          <param name="minid" type="integer" label="Minimum DNA %identity" value="95" min="0" max="100" help="Minimum DNA %identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
          <param name="minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" />
        </when>
        <when value="basic"/>
      </conditional>
    </inputs>
    <outputs>
      <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/>
      <data format="tabular" name="results.mlst.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.mlst.tsv"/>
      <data format="tabular" name="qc_results.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.txt"/>
    </outputs>

    <help><![CDATA[

    ]]></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>

       <citation type="bibtex">
       @UNPUBLISHED{Seemann2016,
       author = "Seemann T",
       title = "MLST: Scan contig files against PubMLST typing schemes",
       year = "2016",
       url = {https://github.com/tseemann/mlst}
      }</citation>
    </citations>
</tool>