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1 <tool id="classify_blast" name="Classify BLAST" version="1.0.0">
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2 <description>results using KronaTools</description>
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3 <command>
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4 ktClassifyBLAST
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5 -o $output
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6 -e $factor
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7 $random
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8 #if $score == 'percentIdentity':
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9 -p
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10 #elif $score == 'bitScore':
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11 -b
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12 #end if
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13 $summarize
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14 #for $input in $inputs
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15 ${input.input}
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16 #end for
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17 </command>
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18
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19 <inputs>
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20 <repeat name="inputs" title="BLAST result">
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21 <param name="input" format="tabular" type="data" label="BLAST result"/>
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22 </repeat>
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23 <param name="factor" type="float" value="10" label="E-value factor" help="For each query, hits with e-values within this factor of the best hit's e-value will be included when computing the lowest common ancestor (or picking randomly)."/>
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24 <param name="random" type="boolean" truevalue="-r" falsevalue="" label="Random" help="Pick from hits within E-value factor randomly instead of finding the lowest common ancestor"/>
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25 <param name="score" type="select" label="Score by">
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26 <option value="evalue">E-value</option>
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27 <option value="percentIdentity">Percent identity</option>
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28 <option value="bitScore">Bit score</option>
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29 </param>
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30 <param name="summarize" type="boolean" truevalue="-s" falsevalue="" label="Summarize" help="Sum results by taxonomy ID and list totals in the first column instead of query IDs"/>
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31 </inputs>
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32
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33 <outputs>
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34 <data format="tabular" name="output"/>
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35 </outputs>
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36
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37 <help>
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38
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39 **What it does**
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40
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41 Creates taxonomic classifications for each query in BLAST results by finding the lowest common ancestor (or by picking randomly, if specified) of "best" hits (as determined by e-value factor above). Requires a KronaTools_ installation (2.0 or higher) with taxonomy downloaded.
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42
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43 .. _KronaTools: http://krona.sourceforge.net
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44
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45 **Input**
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46
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47 Tabular BLAST results containing gi numbers. If comment lines are present, queries with no hits will be assigned to taxon -1 (consistent with MEGAN).
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48
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49 Example input (BLAST)::
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50
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51 1 2 3 4 5 6 7 8 9 10 11 12
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52 read1 gi|211853080|gb|EQ846228.1| 97.33 150 1 3 6 154 9518999 9519146 5e-64 252
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53 read2 gi|211853080|gb|EQ846228.1| 96.69 151 0 5 6 154 9496147 9496294 2e-62 246
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54
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55 **Output**
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56
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57 The output is a list of query IDs (or counts, if **summarize** is specified) followed by NCBI taxonomy IDs and scores. This can be used to create a Krona chart by specifying "Taxonomy ID list" as the **input type**. If the output is summarized, the **summarized** option must also be specified when creating the chart.
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58
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59 Example output (default)::
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60
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61 1 (query ID) 2 (tax ID) 3 (score)
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62 read1 9606 94.34
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63 read2 9616 32.17
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64
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65 Example output (summarized)::
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66
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67 1 (count) 2 (tax ID) 3 (score)
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68 243 9606 94.34
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69 17 9616 32.17
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70
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71 </help>
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72 <requirements>
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73 <requirement type="binary">ktClassifyBLAST</requirement>
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74 </requirements>
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75 </tool>
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