<tool id="confindr" name="confindr" label="Detect sequence contamination using rMLST" version="0.1.3">
    <requirements>
        <requirement type="package" version="0.4.3">confindr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      mkdir in out;
      #if $jobtype.select == "fastq_single"
        perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name;
      #else if $jobtype.select == "fastq_fr"
        perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name;
        perl $__tool_directory__/makein.pl in $jobtype.fastq2 $jobtype.fastq2.name;
      #else if $jobtype.select == "fastq_pair"
        perl $__tool_directory__/makein.pl in $jobtype.coll.forward $jobtype.coll.forward.name;
        perl $__tool_directory__/makein.pl in $jobtype.coll.reverse $jobtype.coll.reverse.name;
      #end if
      confindr.py -i in -o out
      #if $options.select=="advanced"
        #if $options.threads
          -t $options.threads
        #end if
        #if $options.quality
          -q $options.quality
        #end if
        #if $options.basecut
          -b $options.basecut
        #end if
        #if $options.basefrac
          -bf $options.basefrac
        #end if
        #if $options.datatype
          -dt $options.datatype
        #end if
      #else if $options.select=="basic"
        -t \${GALAXY_SLOTS:-1}
      #end if
    ]]></command>
    <inputs>
      <conditional name="jobtype">
        <param name="select" type="select" label="Select Input">
          <option value="fastq_single">Single FASTQ</option>
          <option value="fastq_fr">Forward and Reverse FASTQ</option>
          <option value="fastq_pair">Paired FASTQ Collection</option>
        </param>
        <when value="fastq_single">
          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
        </when>
        <when value="fastq_fr">
          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" />
          <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" />
        </when>
        <when value="fastq_pair">
          <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
        </when>
      </conditional>
      <conditional name="options">
        <param name="select" type="select" label="Basic or Advanced Settings">
          <option value="basic">Basic</option>
          <option value="advanced">Advanced</option>
        </param>
        <when value="advanced">
          <param name="threads" optional="true" type="integer" label="Number of threads (Default=all)" value=""/>
          <param name="quality" optional="true" type="integer" label="Base quality needed to support a multiple allele call (Default=20)" value=""/>
          <param name="basecut" optional="true" type="integer" label="Number of bases necessary to support a multiple allele call (Default=2)" value=""/>
          <param name="basefrac" optional="true" type="float" label="Fraction of bases necessary to support a multiple call." value="">
            <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
          </param>
	  <param name="datatype" type="select" label="Data Type">
            <option value="Illumina">Illumina</option>
            <option value="Nanopore">Nanopore</option>
            <option value="auto">auto</option>
          </param>
        </when>
        <when value="basic">
        </when>
      </conditional>
    </inputs>
    <outputs>
      <data name="output" type="data" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="out/confindr_report.csv" />
    </outputs>
    <help><![CDATA[
    ]]></help>
    <citations>
      <citation type="bibtex">
        @misc{githubconfindr,
        author = {Low,Andrew},
        year = {2018},
        title = {confindr},
        publisher = {GitHub},
        journal = {GitHub repository},
        url = {https://github.com/lowandrew/ConFindr},
      }</citation>
    </citations>
</tool>