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1 <?xml version="1.0"?>
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2 <tool id="bedgraph_to_bigwig" name="bedGraphToBigWig" version="1.0">
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3 <description>Converts a bedGraph file to bigWig format</description>
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4
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5 <macros>
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6 <import>ucsc_macros.xml</import>
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7 </macros>
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8
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9 <requirements>
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10 <requirement type="package" version="340">ucsc_bigwig</requirement>
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11 <requirement type="package" version="340">ucsc_bigbed</requirement>
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12 </requirements>
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13
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 @OPTIONAL_PARAM_FUNC@
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17
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18 ## Allow UCSC track and browser lines in input file
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19 awk '$0 !~ /^(track|browser) /' "${bedgraph_input}" |
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20
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21 #if str($bed_clip) == "bedClip":
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22 bedClip -verbose=2
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23 stdin "${chrominfo_input}" stdout |
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24 #end if
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25
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26 sort -k 1,1 -k 2,2n > "${bedgraph_input}".sorted &&
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27
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28 bedGraphToBigWig
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29 $optional_param("-blockSize", $adv.block_size)
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30 $optional_param("-itemsPerSlot", $adv.items_per_slot)
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31 ${adv.no_compression}
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32 "${bedgraph_input}".sorted "${chrominfo_input}" "${bw_output}"
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33 ]]>
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34 </command>
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35
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36 <expand macro="environment_LC_COLLATE" />
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37
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38 <inputs>
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39 <param name="bedgraph_input" type="data" format="bedgraph"
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40 label="bedGraph input file" />
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41
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42 <param name="chrominfo_input" type="data" format="tabular"
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43 label="Chromosomes sizes file" />
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44
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45 <param name="bed_clip" type="boolean" checked="false"
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46 truevalue="bedClip" falsevalue=""
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47 label="Remove BED items that extend beyond the scaffolds"
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48 help="bedClip" />
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49
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50 <section name="adv" title="Advanced options" expanded="false">
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51 <param name="block_size" type="integer" label="Block size"
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52 min="1" optional="true"
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53 help="Number of items to bundle in r-tree" />
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54
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55 <param name="items_per_slot" type="integer" label="Items per slot"
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56 min="1" optional="true"
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57 help="Number of data points bundled at the lowest level" />
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58
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59 <param name="no_compression" type="boolean" checked="false"
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60 truevalue="-unc" falsevalue=""
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61 label="Do not use compression"
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62 help="-unc" />
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <data name="bw_output" format="bigwig" />
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67 </outputs>
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68 <tests>
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69 <test>
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70 <!-- Test bedGraphToBigWig with default settings -->
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71 <param name="bedgraph_input" value="contigs.bedgraph" ftype="bedgraph" />
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72 <param name="chrominfo_input" value="contigs_chromInfo.tab" ftype="tabular" />
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73 <output name="bw_output" file="contigs.bedgraph.bw" />
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74 </test>
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75 <test>
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76 <!-- Test bedGraphToBigWig with advanced options -->
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77 <param name="bedgraph_input" value="contigs.bedgraph" ftype="bedgraph" />
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78 <param name="chrominfo_input" value="contigs_chromInfo.tab" ftype="tabular" />
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79 <param name="block_size" value="200" />
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80 <param name="items_per_slot" value="500" />
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81 <param name="no_compression" value="-unc" />
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82 <output name="bw_output" file="contigs.bedgraph_advanced.bw" />
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83 </test>
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84 <test>
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85 <!-- Test bedGraphToBigWig with default settings -->
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86 <param name="bedgraph_input" value="contigs.clip.bedGraph" ftype="bedgraph" />
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87 <param name="chrominfo_input" value="contigs_chromInfo.tab" ftype="tabular" />
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88 <param name="bed_clip" value="bedClip" />
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89 <output name="bw_output" file="contigs.bedgraph_clip.bw" />
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90 </test>
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91 </tests>
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92 <help>
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93 <![CDATA[
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94 **What it does**
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95
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96 bedGraphToBigWig converts a `bedGraph <https://genome.ucsc.edu/goldenpath/help/bedgraph.html>`_ file
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97 to the `bigWig format <https://genome.ucsc.edu/goldenpath/help/bigWig.html>`_.
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98
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99 ----
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100
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101 **The bedGraph format**
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102
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103 The first three columns of the bedGraph file are the same as the
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104 `BED format <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_, and it uses
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105 a `zero-start, half-open <http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/>`_
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106 coordinate system. The fourth column of the bedGraph file contains the data values::
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107
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108 chromA chromStartA chromEndA dataValueA
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109 chromB chromStartB chromEndB dataValueB
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110
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111 ----
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112
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113 .. class:: infomark
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114
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115 **Chromosomes sizes file**
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116
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117 This tool requires a chromosomes sizes (``chrom.sizes``) file, which lists the size of
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118 each scaffold within an assembly. For genome assemblies that are hosted by UCSC,
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119 the ``chrom.sizes`` file is available through the
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120 `Sequence and Annotation Downloads <http://hgdownload.cse.ucsc.edu/downloads.html>`_ page.
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121 The `twoBitInfo <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_ tool
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122 can be used to generate the ``chrom.sizes`` for the genome assemblies that are not hosted
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123 by UCSC.
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124
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125 ]]></help>
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126
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127 <expand macro="citations" />
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128 </tool>
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