<tool id="krona" name="Krona chart" version="1.0.0">
<description>of taxonomic abundance</description>
<command>
	#if $type.program == 'galaxy':
		ktImportGalaxy
	#else if $type.program == 'blast':
		ktImportBLAST
	#else
		ktImportTaxonomy
	#end if
	-o $output
	${type.include}
	#if $type.program == 'blast':
		-e ${type.factor}
	#end if
	
	## uncomment for isolated intranets (see README)
	#
	#-u /static/krona
	
	#if $datasets.multiple == 'single':
		$input
	#else
		$datasets.combine
		#for $input in $datasets.inputs
			${input.file},\"${input.name}\"
		#end for
	#end if
</command>

<inputs>
	<conditional name="type">
		<param name="program" label="Input type" type="select">
			<option value="galaxy">Galaxy taxonomic representation</option>
			<option value="blast">Tabular BLAST results</option>
			<option value="taxonomy">Taxonomy ID list</option>
		</param>
		<when value="galaxy">
			<param name="factor" type="hidden" value=""/>
			<param name="include" type="hidden" value=""/>
		</when>
		<when value="blast">
			<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."/>
			<param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits (comment lines must be present in BLAST results)"/>
		</when>
		<when value="taxonomy">
			<param name="factor" type="hidden" value=""/>
			<param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits"/>
		</when>
	</conditional>
	<conditional name="datasets">
		<param name="multiple" type="select" label="Number of datasets">
			<option value="single">Single</option>
			<option value="multiple">Multiple</option>
		</param>
		<when value="single">
			<param name="input" type="data" format="tabular" label="Dataset"/>
		</when>
		<when value="multiple">
			<param
				name="combine"
				type="boolean"
				truevalue="-c"
				falsevalue=""
				label="Combine data sets"
				help="By default, data sets can be stepped through to see varying abundances.  Combining them will sum the data sets at each node to represent total abundances."
			/>
			<repeat name="inputs" title="Data set">
				<param
				name="file"
				format="tabular"
				type="data"
				label="Data"
			/>
				<param name="name" label="Name" type="text">
					<sanitizer>
						<valid initial="string.printable">
							<remove value="&quot;"/>
						</valid>
						<mapping initial="none">
							<add source="&quot;" target="&amp;quot;"/>
						</mapping>
					</sanitizer>
				</param>
			</repeat>
		</when>
	</conditional>
</inputs>

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

<help>

**What it does**

Creates an interactive Krona_ chart of taxonomic abundance. Requires a KronaTools installation (1.3 or higher) with taxonomy downloaded.

 .. _Krona: http://krona.sourceforge.net

**Inputs**

The inputs can be Galaxy taxonomic representations, for example::

  1                     2    3    4         5       6 7 8        9        10            11       12 13               14       15         16          17        18  19  20 21  22  23           24 25
  1L_EYKX4VC01BXWX1_265 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n  Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n   n   n  Homo n  Homo sapiens n  1430919

...or, they can be tabular BLAST results containing gi numbers, which will be used to look up taxonomy IDs and find lowest common ancestors for best hits (comment lines are optional but required for showing queries with no hits in the chart)::

  1                 2                           3       4   5   6   7   8   9       10      11       12
  G58TM3O01ATAI0	gi|211853080|gb|EQ846228.1|	97.33	150	1	3	6	154	9518999	9519146	5e-64	 252
  G58TM3O01ATAI0	gi|211853080|gb|EQ846228.1|	96.69	151	0	5	6	154	9496147	9496294	2e-62	 246
  G58TM3O01ATAI0	gi|211853080|gb|EQ846228.1|	96.69	151	0	5	6	154	9517265	9517412	2e-62	 246

...or, they can be taxonomy IDs with magnitudes (this format can be exported by MEGAN)::

  1     2
  9606  243
  9616  17

...that can optionally have scores::

  1     2    3
  9606  243  94.34
  9616  17   32.17

  </help>
</tool>