view krona.xml @ 3:3398919bc103 draft

Comment tool_dependencies.xml

<tool id="krona" name="Krona chart" version="1.1.0">
<description>of taxonomic abundance</description>
    <requirements>
        <requirement type="package" version="2.2">KronaTools</requirement>
    </requirements>
<command>
	#if $type.program == 'galaxy':
		ktImportGalaxy
	#else if $type.program == 'blast':
		ktImportBLAST
		-e ${type.factor}
		${type.random}
	#else
		ktImportTaxonomy
		${type.summary}
	#end if
	-o $output
	${type.include}
	
	-d $depth

	## 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)"/>
			<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"/>
		</when>
		<when value="taxonomy">
			<param name="factor" type="hidden" value=""/>
			<param name="summary" type="boolean" truevalue="-m 1" falsevalue="" label="Summarized" help="The first column is counts rather than query IDs."/>
			<param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits"/>
		</when>
	</conditional>
	<param name="depth" label="Depth" type="integer" help="The maximum depth to show in the chart (0 for unlimited)." value="0"/>
	<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 (2.0 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
  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

...or, they can be lists of taxonomy IDs preceded by query IDs or counts (these formats can be exported by ktClassifyBLAST or MEGAN), but **Summarized** must be checked if they are counts::

  1	    2
  read1 9606
  read2 9616

Summarized::

  1     2
  243   9606
  17    9616

Both forms can optionally have scores::

  1     2    3
  read1 9606 94.34
  read2 9616 32.17

Summarized::
  
  1     2    3
  243   9606 94.34
  17    9616 32.17

  </help>
  <requirements>
  	<requirement type="binary">ktImportGalaxy</requirement>
  	<requirement type="binary">ktImportBLAST</requirement>
  	<requirement type="binary">ktImportTaxonomy</requirement>
  </requirements>
</tool>