Mercurial > repos > bgruening > deeptools_bigwig_correlate

annotate bigwigCorrelate.xml @ 8:d7961ecf5290 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69
author bgruening
date Wed, 23 Dec 2015 07:26:45 -0500
parents e9e05e3b69fd
children 85c9cda86b1d
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1 <tool id="deeptools_bigwig_correlate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
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2 <description>calculates average read coverages for a list of two or more bigwig files</description>
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3 <macros>
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4 <token name="@BINARY@">bigwigCorrelate</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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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 $mode.region_file
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33 #end if
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34
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35 #if str($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 based on equal length bins.
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47 In the BED file mode, as 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 base pairs 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 (coverages) 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="bigwigCorrelate_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="bamCorrelate_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="bigwigCorrelate_result2.tabular" ftype="tabular" />
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92 <output name="outFileName" file="bigwigCorrelate_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 **What it does**
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98
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99 Given two or more bigWig files, bigwigCorrelate computes the average scores for each of the files in every genomic region.
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100 This analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions
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101 in 'BED-file' mode. Most commonly, the output of bigwigCorrelate is used by other tools such as 'plotCorrelation' or 'plotPCA'
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102 for visualization and diagnostic purposes.
0
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103
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104
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105 **Output files**:
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106
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107 - **Coverage scores**: Coverage scores computed and saved in a format detected by 'plotCorrelation' or 'plotPCA' tools.
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108
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109 - Data matrix (optional,select to save raw counts to a file above): If you want to have a look at the coverage values
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110 or compute statistics yourself using a different program (like R).
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111
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112 -----
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113
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114 @REFERENCES@
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115 ]]>
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116 </help>
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117 <expand macro="citations" />
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118 </tool>