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1 <tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0">
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2 <description>Pathoscioe ID</description>
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3 <requirements>
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2
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4 <requirement type="package" version="2.0.6">pathoscope</requirement>
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5 </requirements>
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3
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6 <command> <![CDATA[pathoscope -h]]> </command>
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7 <inputs>
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8 <param format="sam" name="aligh_file" type="data" label="Align File"/>
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9 <param name="file_type" type="select" label="Choose file type">
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10 <option value="Sam">Sam File</option>
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11 </param>
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12 <param argument="--thetaPrior" type="integer" value="0"
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13 optional="true"
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14 help="EM Algorithm Theta Prior equivalent to adding n non-unique reads" label="thetaPrior">
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15 </param>
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16 <param argument="--piPrior" type="integer" value="0"
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17 optional="true"
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18 help="EM Algorithm Pi Prior equivalent to adding n unique reads" label="piPrior">
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19 </param>
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20 <param name="updatedAlignFile" type="select" label="Generate updated align file?">
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21 <option value="">No</option>
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22 <option value="Yes">Yes</option>
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23 </param>
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24 <param name="displayCutoff" type="select" label="Cutoff display genomes?" value="Yes" help="cutoff display of genomes, even if it is
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25 insignificant">
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26 <option value="">No</option>
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27 <option value="Yes">Yes</option>
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28 </param>
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29 <param name="scoreCutoff" type="integer" value="0" help="Score Cutoff"/>
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30 </inputs>
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31 <outputs>
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32 <data format="tsv" name="tableFile" />
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33 <data format="sam" name="realignFile" />
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34 </outputs>
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35
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36 <tests>
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37 <test>
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38 <param name="input" value="fa_gc_content_input.fa"/>
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39 <output name="out_file1" file="fa_gc_content_output.txt"/>
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40 </test>
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41 </tests>
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42
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43 <help>
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44 Reassigns ambiguous reads, identifies microbial strains
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45 present in the sample, and estimates proportions of
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46 reads from each genome.
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47 </help>
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48
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49 </tool>
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