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<tool id="neptune" name="Neptune: Signature Discovery" version="1.2.5.1">
  <description>Neptune identifies genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.</description>

  <requirements>
    <requirement type="package" version="1.2.5">neptune</requirement>
  </requirements>

  <stdio>
    <exit_code range="1:" />
  </stdio>

  <command>
    neptune

      --inclusion
      #for $i in $inclusion
        "$i"
      #end for

      --exclusion
      #for $i in $exclusion
        "$i"
      #end for

      #if $options.select == "advanced"

        #if $options.kmer:
          --kmer "$options.kmer"
        #end if

        #if $options.rate:
          --rate "$options.rate"
        #end if

        #if $options.exhits:
          --exhits "$options.exhits"
        #end if

        #if $options.size:
          --size "$options.size"
        #end if

      #end if

      --output results

      --parallelization \${GALAXY_SLOTS:-8}

      --organization 3

  </command>

  <inputs>
    <param name="inclusion" type="data_collection" collection_type="list" label="Inclusion" help="The inclusion targets in FASTA format." format="fasta"/>
    <param name="exclusion" type="data_collection" collection_type="list" label="Exclusion" help="The exclusion targets in FASTA format." format="fasta"/>

    <conditional name="options">
      <param name="select" type="select" label="Options Type">
        <option value="basic">Basic</option>
        <option value="advanced">Advanced</option>
      </param>
      <when value="basic">
      </when>
      <when value="advanced">
        <param name="kmer" type="integer" label="k" help="The size of the k-mers. This value is automatically calculated if left blank." optional="true"/>
        <param name="size" type="integer" label="Size" help="The minimum size of reported signatures. The default size is 4k." optional="true"/>
        <param name="rate" type="float" label="Rate" help="The probability of a mutation or error at an arbitrary position. The default value is 0.01." optional="true" value="0.01"/>
        <param name="exhits" type="integer" label="Minimum Exclusion" help="The minimum number of inclusion targets that must contain a k-mer observed in the reference to begin or continue building candidate signatures. This will be calculated if not specified." optional="true"  value="1"/>
      </when>
    </conditional>
  </inputs>

  <outputs>
    <data name="consolidated" from_work_dir="results/consolidated/consolidated.fasta" format="fasta" label="Neptune Signatures: $inclusion.name and $exclusion.name"></data>
    <data name="receipt" from_work_dir="results/receipt.txt" format="txt" label="Neptune Parameters: $inclusion.name and $exclusion.name"></data>
  </outputs>

  <tests>
    <test>
      <output name="receipt"/>
    </test>
  </tests>

  <help>
Neptune locates genomic signatures using an exact k-mer matching strategy while
accommodating k-mer mismatches. The software identifies sequences that are
sufficiently represented within inclusion targets and sufficiently absent from
exclusion targets. The signature discovery process is accomplished using
probabilistic models instead of heuristic strategies.

The inclusion and exclusion targets must be FASTA files.
  </help>

  <citations>
    <citation type="doi">10.1101/032227</citation>
  </citations>

</tool>