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