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comparison hilbertvis.xml @ 0:6f6859904b65 draft

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author devteam
date Tue, 20 Aug 2013 10:57:23 -0400
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1 <tool id="hgv_hilbertvis" name="HVIS" version="1.0.0">
2 <description>visualization of genomic data with the Hilbert curve</description>
3
4 <command interpreter="bash">
5 hilbertvis.sh $input $output $chromInfo "$chrom" $plot_value.score_col $level $mode
6 #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__)
7 1 4 5 7
8 #else
9 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol}
10 #end if
11 </command>
12
13 <inputs>
14 <param name="input" type="data" format="interval,gff" label="Dataset">
15 <validator type="unspecified_build"/>
16 <validator type="metadata" check="chromCol" message="chromCol missing"/>
17 <validator type="metadata" check="startCol" message="startCol missing"/>
18 <validator type="metadata" check="endCol" message="endCol missing"/>
19 </param>
20 <param name="chrom" type="text" label="Sequence to plot" help="Name of sequence (from the chromosome column in the dataset) to plot. If left blank, the first sequence in the dataset will be plotted."/>
21 <conditional name="plot_value">
22 <param name="choice" type="select" label="Value to plot">
23 <option value="score" selected="true">Score column from dataset</option>
24 <option value="exist">Same value for each base (existence)</option>
25 </param>
26 <when value="score">
27 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Score column"/>
28 </when>
29 <when value="exist">
30 <param name="score_col" type="hidden" value="-1"/>
31 </when>
32 </conditional>
33 <param name="level" type="integer" value="9" label="Level" help="Level of Hilbert curve. The resulting image will have 2&lt;sup&gt;level&lt;/sup&gt; by 2&lt;sup&gt;level&lt;/sup&gt; pixels.">
34 <validator type="in_range" min="1" message="The level must be an integer &gt;= 1."/>
35 </param>
36 <param name="mode" type="select" label="Summarization mode" help="Method used to determine a value for a point in the plot which covers multiple values in the input.">
37 <option value="max">Maximal value in each bin</option>
38 <option value="min">Minimal value in each bin</option>
39 <option value="absmax" selected="true">Maximal absolute value in each bin</option>
40 <option value="mean">Mean value of each bin</option>
41 </param>
42 </inputs>
43
44 <outputs>
45 <data name="output" format="pdf"/>
46 </outputs>
47
48 <tests>
49 <test>
50 <param name="input" value="hvis_mkar_chr22.tab"/>
51 <param name="chrom" value="chr22"/>
52 <param name="choice" value="score"/>
53 <param name="score_col" value="15"/>
54 <param name="level" value="9"/>
55 <param name="mode" value="absmax"/>
56 <output name="output" file="hvis_mkar_chr22.pdf" compare="sim_size" delta="7168"/>
57 </test>
58 </tests>
59
60 <help>
61 **Dataset formats**
62
63 The input format is interval_, and the output is an image in PDF format.
64 (`Dataset missing?`_)
65
66 .. _interval: ${static_path}/formatHelp.html#interval
67 .. _Dataset missing?: ${static_path}/formatHelp.html
68
69 -----
70
71 **What it does**
72
73 HilbertVis uses the Hilbert space-filling curve to visualize the structure of
74 position-dependent data. It maps the traditional one-dimensional line
75 visualization onto a two-dimensional square. For example, here is a diagram
76 showing the path of a level-2 Hilbert curve.
77
78 .. image:: ${static_path}/images/hilbertvisDiagram.png
79
80 The shade of each pixel represents the value for the corresponding bin of
81 consecutive genomic positions, calculated according to the specified
82 summarization mode. The pixels are arranged so that bins that are close
83 to each other on the data vector are represented by pixels that are close
84 to each other in the plot. In particular, adjacent bins are mapped to
85 adjacent pixels. Hence, dark spots in a figure represent a peak; the area
86 of the spot in the two-dimensional plot is proportional to the width of the
87 peak in the one-dimensional data, and the darkness of the spot corresponds to
88 the height of the peak.
89
90 The input file is in interval format, and typically contains a column with
91 scores or other numbers, such as conservation scores, SNP density, the
92 coverage of aligned reads from ChIP-Seq data, etc.
93
94 Website: http://www.ebi.ac.uk/huber-srv/hilbert/
95
96 -----
97
98 **Examples**
99
100 Here are some examples from the HilbertVis homepage, using ChIP-Seq data.
101
102 .. image:: ${static_path}/images/hilbertvis1.png
103
104 -----
105
106 .. image:: ${static_path}/images/hilbertvis2.png
107
108 -----
109
110 **Reference**
111
112 Anders S. (2009)
113 Visualization of genomic data with the Hilbert curve.
114 Bioinformatics. 25(10):1231-5. Epub 2009 Mar 17.
115
116 </help>
117 </tool>