diff krona/krona.xml @ 1:42c899125802 default tip

Uploaded

--- a/krona/krona.xml	Wed Sep 21 17:19:28 2011 -0400
+++ b/krona/krona.xml	Mon Mar 19 17:39:59 2012 -0400
@@ -1,29 +1,31 @@
-<tool id="krona" name="Krona chart" version="1.0.0">
+<tool id="krona" name="Krona chart" version="1.1.0">
 <description>of taxonomic abundance</description>
 <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}
-	#if $type.program == 'blast':
-		-e ${type.factor}
-	#end if
 	
+	-d $depth
+
 	## uncomment for isolated intranets (see README)
-	#
-	#-u /static/krona
+	##
+	##-u /static/krona
 	
 	#if $datasets.multiple == 'single':
 		$input
 	#else
 		$datasets.combine
 		#for $input in $datasets.inputs
-			${input.file},\"${input.name}\"
+			${input.file},'${input.name}'
 		#end for
 	#end if
 </command>
@@ -42,12 +44,15 @@
 		<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>
@@ -95,7 +100,7 @@
 
 **What it does**
 
-Creates an interactive Krona_ chart of taxonomic abundance. Requires a KronaTools installation (1.3 or higher) with taxonomy downloaded.
+Creates an interactive Krona_ chart of taxonomic abundance. Requires a KronaTools installation (2.0 or higher) with taxonomy downloaded.
 
  .. _Krona: http://krona.sourceforge.net
 
@@ -108,22 +113,38 @@
 
 ...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
+  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::
 
-...or, they can be taxonomy IDs with magnitudes (this format can be exported by MEGAN)::
+  1	    2
+  read1 9606
+  read2 9616
+
+Summarized::
 
   1     2
-  9606  243
-  9616  17
+  243   9606
+  17    9616
 
-...that can optionally have scores::
+Both forms can optionally have scores::
 
   1     2    3
-  9606  243  94.34
-  9616  17   32.17
+  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>