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author ondovb
date Mon, 19 Mar 2012 17:39:59 -0400
parents e2500c3c8f1b
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0:e2500c3c8f1b 1:42c899125802
1 <tool id="krona" name="Krona chart" version="1.0.0"> 1 <tool id="krona" name="Krona chart" version="1.1.0">
2 <description>of taxonomic abundance</description> 2 <description>of taxonomic abundance</description>
3 <command> 3 <command>
4 #if $type.program == 'galaxy': 4 #if $type.program == 'galaxy':
5 ktImportGalaxy 5 ktImportGalaxy
6 #else if $type.program == 'blast': 6 #else if $type.program == 'blast':
7 ktImportBLAST 7 ktImportBLAST
8 -e ${type.factor}
9 ${type.random}
8 #else 10 #else
9 ktImportTaxonomy 11 ktImportTaxonomy
12 ${type.summary}
10 #end if 13 #end if
11 -o $output 14 -o $output
12 ${type.include} 15 ${type.include}
13 #if $type.program == 'blast':
14 -e ${type.factor}
15 #end if
16 16
17 -d $depth
18
17 ## uncomment for isolated intranets (see README) 19 ## uncomment for isolated intranets (see README)
18 # 20 ##
19 #-u /static/krona 21 ##-u /static/krona
20 22
21 #if $datasets.multiple == 'single': 23 #if $datasets.multiple == 'single':
22 $input 24 $input
23 #else 25 #else
24 $datasets.combine 26 $datasets.combine
25 #for $input in $datasets.inputs 27 #for $input in $datasets.inputs
26 ${input.file},\"${input.name}\" 28 ${input.file},'${input.name}'
27 #end for 29 #end for
28 #end if 30 #end if
29 </command> 31 </command>
30 32
31 <inputs> 33 <inputs>
40 <param name="include" type="hidden" value=""/> 42 <param name="include" type="hidden" value=""/>
41 </when> 43 </when>
42 <when value="blast"> 44 <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."/> 45 <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)"/> 46 <param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits (comment lines must be present in BLAST results)"/>
47 <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"/>
45 </when> 48 </when>
46 <when value="taxonomy"> 49 <when value="taxonomy">
47 <param name="factor" type="hidden" value=""/> 50 <param name="factor" type="hidden" value=""/>
51 <param name="summary" type="boolean" truevalue="-m 1" falsevalue="" label="Summarized" help="The first column is counts rather than query IDs."/>
48 <param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits"/> 52 <param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits"/>
49 </when> 53 </when>
50 </conditional> 54 </conditional>
55 <param name="depth" label="Depth" type="integer" help="The maximum depth to show in the chart (0 for unlimited)." value="0"/>
51 <conditional name="datasets"> 56 <conditional name="datasets">
52 <param name="multiple" type="select" label="Number of datasets"> 57 <param name="multiple" type="select" label="Number of datasets">
53 <option value="single">Single</option> 58 <option value="single">Single</option>
54 <option value="multiple">Multiple</option> 59 <option value="multiple">Multiple</option>
55 </param> 60 </param>
93 98
94 <help> 99 <help>
95 100
96 **What it does** 101 **What it does**
97 102
98 Creates an interactive Krona_ chart of taxonomic abundance. Requires a KronaTools installation (1.3 or higher) with taxonomy downloaded. 103 Creates an interactive Krona_ chart of taxonomic abundance. Requires a KronaTools installation (2.0 or higher) with taxonomy downloaded.
99 104
100 .. _Krona: http://krona.sourceforge.net 105 .. _Krona: http://krona.sourceforge.net
101 106
102 **Inputs** 107 **Inputs**
103 108
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 25 111 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 112 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
108 113
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):: 114 ...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)::
110 115
111 1 2 3 4 5 6 7 8 9 10 11 12 116 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-64 252 117 read1 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-62 246 118 read2 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
115 119
116 ...or, they can be taxonomy IDs with magnitudes (this format can be exported by MEGAN):: 120 ...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::
121
122 1 2
123 read1 9606
124 read2 9616
125
126 Summarized::
117 127
118 1 2 128 1 2
119 9606 243 129 243 9606
120 9616 17 130 17 9616
121 131
122 ...that can optionally have scores:: 132 Both forms can optionally have scores::
123 133
124 1 2 3 134 1 2 3
125 9606 243 94.34 135 read1 9606 94.34
126 9616 17 32.17 136 read2 9616 32.17
137
138 Summarized::
139
140 1 2 3
141 243 9606 94.34
142 17 9616 32.17
127 143
128 </help> 144 </help>
145 <requirements>
146 <requirement type="binary">ktImportGalaxy</requirement>
147 <requirement type="binary">ktImportBLAST</requirement>
148 <requirement type="binary">ktImportTaxonomy</requirement>
149 </requirements>
129 </tool> 150 </tool>