Mercurial > repos > devteam > hgv_hilbertvis
annotate hilbertvis.xml @ 1:de1d3f4e5277 draft
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| author | devteam |
|---|---|
| date | Wed, 21 Aug 2013 13:06:25 -0400 |
| parents | 6f6859904b65 |
| children | e545f2d6795d |
| rev | line source |
|---|---|
| 0 | 1 <tool id="hgv_hilbertvis" name="HVIS" version="1.0.0"> |
| 2 <description>visualization of genomic data with the Hilbert curve</description> | |
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3 <requirements> |
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4 <requirement type="package" version="2.11.0">R</requirement> |
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5 <requirement type="package" version="1.18.0">bioc_hilbertvis</requirement> |
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6 </requirements> |
| 0 | 7 <command interpreter="bash"> |
| 8 hilbertvis.sh $input $output $chromInfo "$chrom" $plot_value.score_col $level $mode | |
| 9 #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__) | |
| 10 1 4 5 7 | |
| 11 #else | |
| 12 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} | |
| 13 #end if | |
| 14 </command> | |
| 15 | |
| 16 <inputs> | |
| 17 <param name="input" type="data" format="interval,gff" label="Dataset"> | |
| 18 <validator type="unspecified_build"/> | |
| 19 <validator type="metadata" check="chromCol" message="chromCol missing"/> | |
| 20 <validator type="metadata" check="startCol" message="startCol missing"/> | |
| 21 <validator type="metadata" check="endCol" message="endCol missing"/> | |
| 22 </param> | |
| 23 <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."/> | |
| 24 <conditional name="plot_value"> | |
| 25 <param name="choice" type="select" label="Value to plot"> | |
| 26 <option value="score" selected="true">Score column from dataset</option> | |
| 27 <option value="exist">Same value for each base (existence)</option> | |
| 28 </param> | |
| 29 <when value="score"> | |
| 30 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Score column"/> | |
| 31 </when> | |
| 32 <when value="exist"> | |
| 33 <param name="score_col" type="hidden" value="-1"/> | |
| 34 </when> | |
| 35 </conditional> | |
| 36 <param name="level" type="integer" value="9" label="Level" help="Level of Hilbert curve. The resulting image will have 2<sup>level</sup> by 2<sup>level</sup> pixels."> | |
| 37 <validator type="in_range" min="1" message="The level must be an integer >= 1."/> | |
| 38 </param> | |
| 39 <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."> | |
| 40 <option value="max">Maximal value in each bin</option> | |
| 41 <option value="min">Minimal value in each bin</option> | |
| 42 <option value="absmax" selected="true">Maximal absolute value in each bin</option> | |
| 43 <option value="mean">Mean value of each bin</option> | |
| 44 </param> | |
| 45 </inputs> | |
| 46 | |
| 47 <outputs> | |
| 48 <data name="output" format="pdf"/> | |
| 49 </outputs> | |
| 50 | |
| 51 <tests> | |
| 52 <test> | |
| 53 <param name="input" value="hvis_mkar_chr22.tab"/> | |
| 54 <param name="chrom" value="chr22"/> | |
| 55 <param name="choice" value="score"/> | |
| 56 <param name="score_col" value="15"/> | |
| 57 <param name="level" value="9"/> | |
| 58 <param name="mode" value="absmax"/> | |
| 59 <output name="output" file="hvis_mkar_chr22.pdf" compare="sim_size" delta="7168"/> | |
| 60 </test> | |
| 61 </tests> | |
| 62 | |
| 63 <help> | |
| 64 **Dataset formats** | |
| 65 | |
| 66 The input format is interval_, and the output is an image in PDF format. | |
| 67 (`Dataset missing?`_) | |
| 68 | |
| 69 .. _interval: ${static_path}/formatHelp.html#interval | |
| 70 .. _Dataset missing?: ${static_path}/formatHelp.html | |
| 71 | |
| 72 ----- | |
| 73 | |
| 74 **What it does** | |
| 75 | |
| 76 HilbertVis uses the Hilbert space-filling curve to visualize the structure of | |
| 77 position-dependent data. It maps the traditional one-dimensional line | |
| 78 visualization onto a two-dimensional square. For example, here is a diagram | |
| 79 showing the path of a level-2 Hilbert curve. | |
| 80 | |
| 81 .. image:: ${static_path}/images/hilbertvisDiagram.png | |
| 82 | |
| 83 The shade of each pixel represents the value for the corresponding bin of | |
| 84 consecutive genomic positions, calculated according to the specified | |
| 85 summarization mode. The pixels are arranged so that bins that are close | |
| 86 to each other on the data vector are represented by pixels that are close | |
| 87 to each other in the plot. In particular, adjacent bins are mapped to | |
| 88 adjacent pixels. Hence, dark spots in a figure represent a peak; the area | |
| 89 of the spot in the two-dimensional plot is proportional to the width of the | |
| 90 peak in the one-dimensional data, and the darkness of the spot corresponds to | |
| 91 the height of the peak. | |
| 92 | |
| 93 The input file is in interval format, and typically contains a column with | |
| 94 scores or other numbers, such as conservation scores, SNP density, the | |
| 95 coverage of aligned reads from ChIP-Seq data, etc. | |
| 96 | |
| 97 Website: http://www.ebi.ac.uk/huber-srv/hilbert/ | |
| 98 | |
| 99 ----- | |
| 100 | |
| 101 **Examples** | |
| 102 | |
| 103 Here are some examples from the HilbertVis homepage, using ChIP-Seq data. | |
| 104 | |
| 105 .. image:: ${static_path}/images/hilbertvis1.png | |
| 106 | |
| 107 ----- | |
| 108 | |
| 109 .. image:: ${static_path}/images/hilbertvis2.png | |
| 110 | |
| 111 ----- | |
| 112 | |
| 113 **Reference** | |
| 114 | |
| 115 Anders S. (2009) | |
| 116 Visualization of genomic data with the Hilbert curve. | |
| 117 Bioinformatics. 25(10):1231-5. Epub 2009 Mar 17. | |
| 118 | |
| 119 </help> | |
| 120 </tool> |