<tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0">
  <description>Pathoscope ID</description>
<requirements>
    <requirement type="package" version="2.0.6">pathoscope</requirement>
</requirements>
<command> <![CDATA[ln -s '$alignFile' align.sam &&
  pathoscope ID -alignFile align.sam -fileType $fileType -piPrior $piPrior -thetaPrior $thetaPrior
  -scoreCutoff $scoreCutoff -emEpsilon $emEpsilon -maxIter $maxIter
  #unless $updatedAlignFile
    --noUpdatedAlignFile
  #end unless
  #unless $displayCutoff
    --noDisplayCutoff
  #end unless
  #if $outMatrix
    --outMatrix
  #end if]]>
</command>
<inputs>
  <param format="sam" name="alignFile" type="data" label="Align File"/>
  <param name="fileType" type="select" label="Choose file type">
    <option value="sam">Sam File</option>
  </param>
  <param name="thetaPrior" type="integer" value="0"
    optional="true"
    help="EM Algorithm Theta Prior equivalent to adding n non-unique reads" label="thetaPrior">
  </param>
  <param name="piPrior" type="integer" value="0"
    optional="true"
    help="EM Algorithm Pi Prior equivalent to adding n unique reads" label="piPrior">
  </param>
  <param name="updatedAlignFile" type="boolean" truevalue="yes" falsevalue="no" checked="on" label="Generate updated align file?"/>
  <param name="displayCutoff" type="boolean" truevalue="yes" falsevalue="no" checked="on" label="Cutoff display genomes?" help="cutoff display of genomes, even if it is insignificant"/>
  <param name="outMatrix" type="boolean" truevalue="yes" falsevalue="no" checked="off" label="Output alignment matrix"/>
  <param name="scoreCutoff" type="float" value="0.01" help="Score Cutoff"/>
  <param name="emEpsilon" type="float" value="1e-7" help="EM Algorithm Epsilon cutoff"/>
  <param name="maxIter" type="integer" value="50" help="EM Algorithm maximum iterations"/>
</inputs>
<outputs>
  <data format="tsv" name="tableFile" from_work_dir="pathoid-sam-report.tsv" />
  <data format="sam" name="realignFile" from_work_dir="updated_align.sam" />
</outputs>

<tests>
  <test>
    <param name="alignFile" value="MAP_3852_align.sam"/>
    <param name="fileType" value="sam" />
    <param name="thetaPrior" value="0" />
    <param name="piPrior" value="0" />
    <param name="updatedAlignFile" checked="on" />
    <param name="displayCutoff" checked="on" />
    <param name="outMatrix" checked="off" />
    <param name="scoreCutoff" value="0.01" />
    <param name="emEpsilon" value="1e-7" />
    <param name="maxIter" value="50" />
    <output name="tsv" file="pathoid-sam-report.tsv"/>
    <output name="sam" file="updated_align.sam"/>
  </test>
</tests>

<help>
The PathoID module is the core of the PathoScope pipeline. The key is to identify
reads with unique alignments and use them to guide the reassignment of reads with ambiguous
alignments.
</help>
<citations>
  <citation type="doi">10.1101/gr.150151.112</citation>
  <citation type="doi">10.1186/2049-2618-2-33</citation>
  <citation type="doi">10.1186/1471-2105-15-262</citation>
  <citation type="doi">10.4137/CIN.S13890</citation>
</citations>

</tool>