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