Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

annotate multiBigwigSummary.xml @ 4:224ca3519864 draft

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author bgruening
date Thu, 10 Mar 2016 03:22:58 -0500
parents 3da3c3750962
children 7b4732d497a3
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1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0">
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2 <description>calculates average scores for a list of two or more bigwig files</description>
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3 <macros>
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4 <token name="@BINARY@">multiBigwigSummary</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 #set files=[]
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11 #set labels=[]
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12
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13 @multiple_input_bigwigs@
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15 @BINARY@
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16 $mode.modeOpt
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18 @THREADS@
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20 --outFileName $outFile
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21 --bwfiles '#echo "' '".join($files)#'
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22 --labels '#echo "' '".join($labels)#'
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24 #if $outRawCounts:
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25 --outRawCounts '$outFileRawCounts'
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26 #end if
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28 #if $mode.modeOpt == "bins":
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29 --binSize '$mode.binSize'
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30 --distanceBetweenBins '$mode.distanceBetweenBins'
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31 #else:
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32 --BED $mode.region_file
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33 #end if
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35 #if str($region.value) != '':
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36 --region '$region'
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37 #end if
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38 ]]>
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39 </command>
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40
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41 <inputs>
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42 <expand macro="multiple_input_bigwigs" />
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43
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44 <conditional name="mode">
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45 <param name="modeOpt" type="select" label="Choose computation mode"
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46 help="In the bins mode, the correlation is computed using equally sized bins.
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47 In the BED file mode, a list of genomic regions in BED format has to be given.
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48 For each region in the BED file, the number of overlapping reads is counted in
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49 each of the BigWig files. Then the correlation is computed.">
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50 <option value="bins" selected="true">Bins</option>
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51 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
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52 </param>
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53 <when value="bins">
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54 <param name="binSize" type="integer" value="10000" min="1"
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55 label="Bin size in bp"
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56 help="Length in bases for a window used to sample the genome. (--binSize)"/>
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57
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58 <expand macro="distanceBetweenBins" />
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59 </when>
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60 <when value="BED-file">
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61 <param name="region_file" type="data" format="bed"
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62 label="Region file in BED format"
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63 help="Correlation is computed for the number of reads that overlap such regions."/>
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64 </when>
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65 </conditional>
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66
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67 <expand macro="region_limit_operation" />
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68 <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>
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69
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70 </inputs>
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71 <outputs>
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72 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
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73 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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74 <filter>outRawCounts is True</filter>
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75 </data>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
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80 <param name="modeOpt" value="bins" />
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81 <param name="binSize" value="10" />
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82 <param name="corMethod" value="spearman" />
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83 <output name="outFileName" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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84 </test>
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85 <!--test>
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86 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
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87 <param name="modeOpt" value="BED-file" />
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88 <param name="region_file" value="multiBamSummary_regions.bed" />
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89 <param name="corMethod" value="pearson" />
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90 <param name="outRawCounts" value="True" />
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91 <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
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92 <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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93 </test-->
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94 </tests>
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95 <help>
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96 <![CDATA[
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97
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98 What it does
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99 --------------
0
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100
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101 This tool computes the average scores for every genomic region for every bigWig file that is provided. In principle, it does the same as ``multiBamSummary``, but for bigWig files.
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102
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103 The analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions (e.g., genes) in 'BED-file' mode.
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104
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105 Typically the output of ``multiBigwigSummary`` is used by other tools, such as ``plotCorrelation`` or ``plotPCA``, for visualization and diagnostic purposes.
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106
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107
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108 Output
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109 --------
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110
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111 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``.
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112
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113 To analyze the average scores yourself, you can get the **uncompressed score matrix** where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file). (To obtain this output file, select "Save raw counts (coverages) to file" )
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114
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115 .. image:: $PATH_TO_IMAGES/multiBigwigSummary_output.png
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116 :width: 600
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117 :height: 358
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118
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119 -----
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120
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121 @REFERENCES@
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122 ]]>
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123 </help>
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124 <expand macro="citations" />
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125 </tool>