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comparison krona/krona.xml @ 0:e2500c3c8f1b

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author ondovb
date Wed, 21 Sep 2011 17:19:28 -0400
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1 <tool id="krona" name="Krona chart" version="1.0.0">
2 <description>of taxonomic abundance</description>
3 <command>
4 #if $type.program == 'galaxy':
5 ktImportGalaxy
6 #else if $type.program == 'blast':
7 ktImportBLAST
8 #else
9 ktImportTaxonomy
10 #end if
11 -o $output
12 ${type.include}
13 #if $type.program == 'blast':
14 -e ${type.factor}
15 #end if
16
17 ## uncomment for isolated intranets (see README)
18 #
19 #-u /static/krona
20
21 #if $datasets.multiple == 'single':
22 $input
23 #else
24 $datasets.combine
25 #for $input in $datasets.inputs
26 ${input.file},\"${input.name}\"
27 #end for
28 #end if
29 </command>
30
31 <inputs>
32 <conditional name="type">
33 <param name="program" label="Input type" type="select">
34 <option value="galaxy">Galaxy taxonomic representation</option>
35 <option value="blast">Tabular BLAST results</option>
36 <option value="taxonomy">Taxonomy ID list</option>
37 </param>
38 <when value="galaxy">
39 <param name="factor" type="hidden" value=""/>
40 <param name="include" type="hidden" value=""/>
41 </when>
42 <when value="blast">
43 <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."/>
44 <param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits (comment lines must be present in BLAST results)"/>
45 </when>
46 <when value="taxonomy">
47 <param name="factor" type="hidden" value=""/>
48 <param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits"/>
49 </when>
50 </conditional>
51 <conditional name="datasets">
52 <param name="multiple" type="select" label="Number of datasets">
53 <option value="single">Single</option>
54 <option value="multiple">Multiple</option>
55 </param>
56 <when value="single">
57 <param name="input" type="data" format="tabular" label="Dataset"/>
58 </when>
59 <when value="multiple">
60 <param
61 name="combine"
62 type="boolean"
63 truevalue="-c"
64 falsevalue=""
65 label="Combine data sets"
66 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."
67 />
68 <repeat name="inputs" title="Data set">
69 <param
70 name="file"
71 format="tabular"
72 type="data"
73 label="Data"
74 />
75 <param name="name" label="Name" type="text">
76 <sanitizer>
77 <valid initial="string.printable">
78 <remove value="&quot;"/>
79 </valid>
80 <mapping initial="none">
81 <add source="&quot;" target="&amp;quot;"/>
82 </mapping>
83 </sanitizer>
84 </param>
85 </repeat>
86 </when>
87 </conditional>
88 </inputs>
89
90 <outputs>
91 <data format="html" name="output"/>
92 </outputs>
93
94 <help>
95
96 **What it does**
97
98 Creates an interactive Krona_ chart of taxonomic abundance. Requires a KronaTools installation (1.3 or higher) with taxonomy downloaded.
99
100 .. _Krona: http://krona.sourceforge.net
101
102 **Inputs**
103
104 The inputs can be Galaxy taxonomic representations, for example::
105
106 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
107 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
108
109 ...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)::
110
111 1 2 3 4 5 6 7 8 9 10 11 12
112 G58TM3O01ATAI0 gi|211853080|gb|EQ846228.1| 97.33 150 1 3 6 154 9518999 9519146 5e-64 252
113 G58TM3O01ATAI0 gi|211853080|gb|EQ846228.1| 96.69 151 0 5 6 154 9496147 9496294 2e-62 246
114 G58TM3O01ATAI0 gi|211853080|gb|EQ846228.1| 96.69 151 0 5 6 154 9517265 9517412 2e-62 246
115
116 ...or, they can be taxonomy IDs with magnitudes (this format can be exported by MEGAN)::
117
118 1 2
119 9606 243
120 9616 17
121
122 ...that can optionally have scores::
123
124 1 2 3
125 9606 243 94.34
126 9616 17 32.17
127
128 </help>
129 </tool>