I've added the metaphlan2krona.py script to the metaphlan toolshed repo.
diff -r e88fa24fa837 metaphlan.xml
--- a/metaphlan.xml
Wed Jun 06 10:41:23 2012 -0400
+++ b/metaphlan.xml
Wed Aug 22 21:36:21 2012 -0400
@@ -14,7 +14,7 @@
</command>
<inputs>
-
<param format="fasta" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
+
<param format="fasta,fastq,fastqsanger" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
<param name="PresetsForBowtie2" type="select" format="text">
<label>Sensitivity options for read-marker similarity (as described by BowTie2)</label>
<option value="very-sensitive-local">Very Sensitive Local</option>
diff -r e88fa24fa837 metaphlan2krona.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan2krona.py
Wed Aug 22 21:36:21 2012 -0400
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+# ==============================================================================
+# Conversion script: from MetaPhlAn output to Krona text input file
+# ==============================================================================
+
+import sys
+import optparse
+import re
+
+def main():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option( '-p', '--profile', dest='profile', default='', action='store', help='The input file is the MetaPhlAn standard result file' )
+ parser.add_option( '-k', '--krona', dest='krona', default='krona.out', action='store', help='the Krons output file name' )
+ ( options, spillover ) = parser.parse_args()
+
+ if not options.profile or not options.krona:
+ parser.print_help()
+ sys.exit()
+
+ re_candidates = re.compile(r"s__|unclassified\t")
+ re_replace = re.compile(r"\w__")
+ re_bar = re.compile(r"\|")
+
+ metaPhLan = list()
+ with open(options.profile,'r') as f:
+ metaPhLan = f.readlines()
+ f.close()
+
+ krona_tmp = options.krona
+ metaPhLan_FH = open(krona_tmp, 'w')
+
+ for aline in (metaPhLan):
+ if(re.search(re_candidates, aline)):
+ x=re.sub(re_replace, '\t', aline)
+ x=re.sub(re_bar, '', x)
+
+ x_cells = x.split('\t')
+ lineage = '\t'.join(x_cells[0:(len(x_cells) -1)])
+ abundance = float(x_cells[-1].rstrip('\n'))
+
+ metaPhLan_FH.write('%s\n'%(str(abundance) + '\t' + lineage))
+
+ metaPhLan_FH.close()
+
+if __name__ == '__main__':
+ main()
diff -r e88fa24fa837 metaphlan_to_krona.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan_to_krona.xml
Wed Aug 22 21:36:21 2012 -0400
@@ -0,0 +1,17 @@
+<tool id="meta_to_krona" name="MetaPhlAn to Krona" version="1.0.0">
+ <description>Converter</description>
+ <command interpreter="python">
+metaphlan2krona.py -p $input -k $output
+ </command>
+ <inputs>
+ <param name="input" type="data" format="tabular" label="Input MetaPhlAn File"/>
+ </inputs>
+ <outputs>
+ <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+ MetaPhlAn to Krona Converter
+ </help>
+</tool>
diff -r 42c899125802 krona/krona.xml
--- a/krona/krona.xml
Mon Mar 19 17:39:59 2012 -0400
+++ b/krona/krona.xml
Wed Aug 22 21:39:17 2012 -0400
@@ -7,15 +7,18 @@
ktImportBLAST
-e ${type.factor}
${type.random}
+ #else if $type.program == 'krona':
+ ktImportText
#else
ktImportTaxonomy
${type.summary}
#end if
- -o $output
+ -o $output
${type.include}
+ #unless $type.program == 'krona'
+ -d $depth
+ #end unless
- -d $depth
-
## uncomment for isolated intranets (see README)
##
##-u /static/krona
@@ -36,6 +39,7 @@
<option value="galaxy">Galaxy taxonomic representation</option>
<option value="blast">Tabular BLAST results</option>
<option value="taxonomy">Taxonomy ID list</option>
+ <option value="krona">Krona format</option>
</param>
<when value="galaxy">
<param name="factor" type="hidden" value=""/>
@@ -51,6 +55,10 @@
<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>
+ <when value="krona">
+
<param name="factor" type="hidden" value=""/>
+
<param name="include" type="hidden" value=""/>
+ </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">
one more item.. had to add