<tool id="classify_blast" name="Classify BLAST" version="1.0.0">
<description>results using KronaTools</description>
<command>
	ktClassifyBLAST
	-o $output
	-e $factor
	$random
	#if $score == 'percentIdentity':
		-p
	#elif $score == 'bitScore':
		-b
	#end if
	$summarize
	#for $input in $inputs
		${input.input}
	#end for
</command>

<inputs>
	<repeat name="inputs" title="BLAST result">
		<param name="input" format="tabular" type="data" label="BLAST result"/>
	</repeat>
	<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)."/>
	<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"/>
	<param name="score" type="select" label="Score by">
		<option value="evalue">E-value</option>
		<option value="percentIdentity">Percent identity</option>
		<option value="bitScore">Bit score</option>
	</param>
	<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"/>
</inputs>

<outputs>
	<data format="tabular" name="output"/>
</outputs>

<help>

**What it does**

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.

 .. _KronaTools: http://krona.sourceforge.net

**Input**

Tabular BLAST results containing gi numbers. If comment lines are present, queries with no hits will be assigned to taxon -1 (consistent with MEGAN).

Example input (BLAST)::

  1      2                            3      4    5  6  7  8    9        10       11     12
  read1  gi|211853080|gb|EQ846228.1|  97.33  150  1  3  6  154  9518999  9519146  5e-64  252
  read2  gi|211853080|gb|EQ846228.1|  96.69  151  0  5  6  154  9496147  9496294  2e-62  246

**Output**

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.

Example output (default)::

  1 (query ID)  2 (tax ID)  3 (score)
  read1         9606        94.34
  read2         9616        32.17

Example output (summarized)::

  1 (count)  2 (tax ID)  3 (score)
  243        9606        94.34
  17         9616        32.17

</help>
  <requirements>
  	<requirement type="binary">ktClassifyBLAST</requirement>
  </requirements>
</tool>