view PathID.xml @ 4:c849d1e6ee3e draft

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<tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0">
  <description>Pathoscioe ID</description>
<requirements>
    <requirement type="package" version="2.0.6">pathoscope</requirement>
</requirements>
<command> <![CDATA[pathoscope -h]]>  </command>
  <inputs>
    <param format="sam" name="aligh_file" type="data" label="Align File"/>
    <param name="file_type" type="select" label="Choose file type">
      <option value="Sam">Sam File</option>
    </param>
    <param argument="--thetaPrior" type="integer" value="0"
      optional="true"
      help="EM Algorithm Theta Prior equivalent to adding n non-unique reads" label="thetaPrior">
    </param>
    <param argument="--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="select" label="Generate updated align file?">
        <option value="">No</option>
        <option value="Yes">Yes</option>
    </param>
      <param name="displayCutoff" type="select" label="Cutoff display genomes?" value="Yes" help="cutoff display of genomes, even if it is
                          insignificant">
          <option value="">No</option>
          <option value="Yes">Yes</option>
      </param>
      <param name="scoreCutoff" type="integer" value="0" help="Score Cutoff"/>
  </inputs>
  <outputs>
    <data format="tsv" name="tableFile" />
    <data format="sam" name="realignFile" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>

  <help>
Reassigns ambiguous reads, identifies microbial strains
present in the sample, and estimates proportions of
reads from each genome.
  </help>

</tool>