<tool id="ococo" name="ococo" version="0.1.2.6" >
    <description>consensus caller on SAM/BAM</description>
    <requirements>
      <requirement type="package" version="0.1.2.6">ococo</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
    ococo -i '$input_alignment'
    #if $fasta_reference:
        --fasta-ref '$fasta_reference'
    #end if
    --counters $counters
    --strategy $strategy
    --min-MQ $min_mq
    --min-BQ $min_bq
    --ref-weight $ref_weight
    --min-cov $min_cov
    --maj-thres $maj_thres
    #for $out in str($save_output).split(','):
        #if str($out) == 'vcf':
            --vcf-cons $vcf_cons
        #elif str($out) == 'fasta':
            --fasta-cons $fasta_cons
        #elif str($out) == 'pileup':
            --pileup $pileup
        #end if
    #end for
]]>
    </command>
    <inputs>
      <param name="input_alignment" type="data" format="bam,sam" label="SAM/BAM dataset"/>
      <param name="fasta_reference" type="data" format="fasta" label="Select fasta reference" optional="True"/>
      <param name="counters" type="select" label="Counter configuration: [ococo16]">
        <option value="ococo16">ococo16 (3b/counter, 16b/position)</option>
        <option value="ococo32">ococo32 (7b/counter, 32b/position)</option>
        <option value="ococo64">ococo64 (15b/counter, 64b/position)</option>
      </param>
      <param name="strategy" type="select" label="Strategy for updates: [majority]">
        <option value="majority">Majority (update to majority base)</option>
        <option value="stochastic">stochastic (update to stochastically drawn base)</option>
      </param>

      <param name="save_output" type="select" label="Save output(s)" optional="False" multiple="True" help="Determine which output file(s) to keep">
        <option value="vcf">Consensus VCF</option>
        <option value="fasta">Consensus Fasta</option>
        <option value="pileup">Pileup</option>
      </param>
      
      <param name="min_mq" type="integer" label="Minimum mapping quality score" help="skip alignments with mapping quality smaller than INT [1]" value="1" argument="min-MQ"/>
      <param name="min_bq" type="integer" label="Minimum base quality score" help="skip bases with base quality smaller than INT [13]" value="13" argument="--min-BQ"/>
      <param name="ref_weight" type="integer" label="Initial nucleotides counter" help="initial counter value for nucleotides from ref [0]" value="0" argument='--ref-weight'/>
      <param name="min_cov" type="integer" label="Minimum coverage required" help="minimum coverage required for update [2]" value="2" argument="--min-cov"/>
      <param name="maj_thres" type="float" label="Majority consensus threshold [0.51]"  value="0.51" argument="--maj-thres"/>
    </inputs>

    <outputs>
      <data name="vcf_cons" format="vcf" label="VCF Consensus on ${input_alignment.name}">
        <filter>'vcf' in save_output</filter>
      </data>
      <data name="fasta_cons" format="fasta" label="Fasta Consensus on ${input_alignment.name}">
        <filter>'fasta' in save_output</filter>
      </data>
      <data name="pileup" format="pileup" label="Pileup on ${input_alignment.name}">
        <filter>'pileup' in save_output</filter>
      </data>
    </outputs>
    <tests>
      <test>
        <param name="input_alignment" value="alignment_A_2.sam"/>
        <param name="fasta_reference" value="reference.fa"/>
        <param name="save_output" value="vcf,fasta,pileup"/>
        <output name="fasta_cons" value="answer.fa"/>
        <output name="pileup" value="answer.pileup"/>
        <output name="vcf_cons">
          <assert_contents>
            <has_text text="AF=1.00;CS=2,0,0,0;COV=2"/>
          </assert_contents>
        </output>
      </test>
    </tests>
    <help>
<![CDATA[

**OCOCO - Online Consensus Caller**

OCOCO is a online consensus caller, capable to infer SNVs dynamically as read alignments are fed in.
OCOCO inputs unsorted alignments from an unsorted SAM/BAM stream and decides about single-nucleotide
updates of the current genomic consensus using statistics stored in compact several-bits counters.
Updates are reported in the online fashion using unsorted VCF. OCOCO provides a fast and
memory-efficient alternative to the usual variant calling, particularly advantageous when reads
are sequenced or mapped progressively, or when available computational resources are at a premium. 

]]>      
    </help>
    <citations>
      <citation type="bibtex">
        @misc{1207.3907,
        Author = {Karel Brinda},
        Title = {Ococo: an online consensus caller},
        Year = {2017},
        Eprint = {arXiv:1712.01146},
        url = {https://arxiv.org/abs/1712.01146}
        }
      </citation>
    </citations>
</tool>