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1 <tool id="bigwigCompare" name="bigwigCompare" version="1.0">
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2 <description>compares two bigwig files based on the number of mapped reads</description>
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3
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4 <command>
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5 bigwigCompare
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6 --bigwig1 '$bigwigFile1'
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7 --bigwig2 '$bigwigFile2'
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8
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9 --outFileName '$outFileName'
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10 --outFileFormat '$outFileFormat'
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11
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12 --ratio $comparison_type
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13
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14 #if $advancedOpt.showAdvancedOpt == "yes":
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15 #if str($advancedOpt.region.value) != '':
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16 --region '$advancedOpt.region'
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17 #end if
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18
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19 --missingDataAsZero $advancedOpt.missingDataAsZero
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20 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
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21 --pseudocount '$advancedOpt.pseudocount'
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22 --binSize $advancedOpt.binSize
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23
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24 #end if
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25 --numberOfProcessors 4
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26
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27
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28 </command>
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29
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30 <inputs>
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31 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
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32
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33 <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" />
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34
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35 <param name="comparison_type" type="select"
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36 label="How to compare the two files"
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37 help="The reciprocal ratio returns the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative fold changes." >
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38 <option value="log2" selected="true">log2 ratio</option>
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39 <option value="ratio">simple ratio</option>
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40 <option value="subtract">difference (subtract input from treatment)</option>
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41 <option value="add">sum</option>
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42 <option value="reciprocal_ratio">reciprocal ratio</option>
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43 </param>
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44
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45
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46
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47 <param name="outFileFormat" type="select" label="Coverage file format">
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48 <option value="bigwig" selected="true">bigwig</option>
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49 <option value="bedgraph">bedgraph</option>
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50 </param>
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51
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52 <conditional name="advancedOpt">
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53 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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54 <option value="no" selected="true">no</option>
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55 <option value="yes">yes</option>
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56 </param>
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57 <when value="no" />
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58 <when value="yes">
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59
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60 <param name="binSize" type="integer" value="50" min="1"
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61 label="Bin size in bp"
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62 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/>
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63
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64 <param name="region" type="text" value=""
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65 label="Region of the genome to limit the operation to"
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66 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" />
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67
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68 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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69 label ="Treat missing data as zero"
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70 help ="This parameter determines if missing data should be replaced with a zero. If set to "no", missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." />
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71
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72 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/>
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73 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/>
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74 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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75
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76 </when>
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77 </conditional>
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78
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79 </inputs>
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80 <outputs>
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81 <data format="bigwig" name="outFileName">
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82 <change_format>
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83 <when input="outFileFormat" value="bigwig" format="bigwig" />
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84 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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85 </change_format>
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86 </data>
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87 </outputs>
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88
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89 <requirements>
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90 <requirement type="python-module">argsparse</requirement>
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91 <requirement type="python-module">pysam</requirement>
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92 <requirement type="python-module">numpy</requirement>
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93 </requirements>
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94
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95 <help>
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96
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97 **What it does**
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98
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99 This tool compares two bigwig files based on the number of mapped reads. To
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100 compare the bigwig files the genome is partitioned into bins of equal size,
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101 then the number of reads found in each BAM file are counted for such bins and
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102 finally a summarizing value is reported. This vaule can be the ratio of the
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103 number of readsper bin, the log2 of the ratio, the sum or the difference.
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104
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105 -----
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106
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107 .. class:: infomark
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108
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109 Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
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110
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111 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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112
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113
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114 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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115 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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116 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
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117
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118 </help>
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119
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120 </tool>
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