Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

annotate multiBigwigSummary.xml @ 16:9cd1cde06157 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c
author bgruening
date Mon, 05 Feb 2018 11:42:07 -0500
parents 2565fa4fe087
children 97efbac65e5e
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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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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 $outFile
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22 --bwfiles '#echo "' '".join($files)#'
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23 --labels #echo " ".join($labels)#
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25 #if $outRawCounts:
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26 --outRawCounts '$outFileRawCounts'
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27 #end if
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29 #if $mode.modeOpt == "bins":
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30 --binSize '$mode.binSize'
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31 --distanceBetweenBins '$mode.distanceBetweenBins'
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32 #else:
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33 --BED $mode.region_file
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34 #end if
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36 #if str($region.value) != '':
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37 --region '$region'
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38 #end if
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40 #if $advancedOpt.showAdvancedOpt == "yes":
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41 @ADVANCED_OPTS_GTF@
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42 @blacklist@
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43 #end if
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44 ]]>
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45 </command>
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47 <inputs>
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48 <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/>
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49
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50 <conditional name="mode">
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51 <param name="modeOpt" type="select" label="Choose computation mode"
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52 help="In the bins mode, the correlation is computed using equally sized bins.
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53 In the BED file mode, a list of genomic regions in BED format has to be given.
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54 For each region in the BED file, the number of overlapping reads is counted in
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55 each of the BigWig files. Then the correlation is computed.">
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56 <option value="bins" selected="true">Bins</option>
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57 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
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58 </param>
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59 <when value="bins">
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60 <param name="binSize" type="integer" value="10000" min="1"
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61 label="Bin size in bp"
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62 help="Length in bases for a window used to sample the genome. (--binSize)"/>
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63
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64 <expand macro="distanceBetweenBins" />
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65 </when>
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66 <when value="BED-file">
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67 <param name="region_file" type="data" format="bed,gtf"
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68 label="Region file in BED format"
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69 help="Correlation is computed for the number of reads that overlap such regions."/>
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70 </when>
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71 </conditional>
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72
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73 <expand macro="region_limit_operation" />
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74 <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>
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75
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76 <expand macro="advancedOpt_scaffold">
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77 <expand macro="gtf_options" />
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78 <expand macro="blacklist" />
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79 </expand>
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80
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81 </inputs>
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82 <outputs>
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83 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
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84 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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85 <filter>outRawCounts is True</filter>
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86 </data>
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87 </outputs>
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88 <tests>
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89 <test>
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90 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
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91 <param name="modeOpt" value="bins" />
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92 <param name="binSize" value="10" />
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93 <param name="corMethod" value="spearman" />
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94 <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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95 </test>
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96 <!--test>
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97 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
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98 <param name="modeOpt" value="BED-file" />
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99 <param name="region_file" value="multiBamSummary_regions.bed" />
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100 <param name="corMethod" value="pearson" />
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101 <param name="outRawCounts" value="True" />
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102 <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
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103 <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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104 </test-->
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105 </tests>
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106 <help>
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107 <![CDATA[
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108
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109 What it does
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110 --------------
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111
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112 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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113
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114 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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115
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116 Typically the output of ``multiBigwigSummary`` is used by other tools, such as ``plotCorrelation`` or ``plotPCA``, for visualization and diagnostic purposes.
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117
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118
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119 Output
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120 --------
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121
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122 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``.
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123
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124 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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125
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126 .. image:: $PATH_TO_IMAGES/multiBigwigSummary_output.png
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127 :width: 600
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128 :height: 358
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129
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130 -----
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131
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132 @REFERENCES@
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133 ]]>
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134 </help>
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135 <expand macro="citations" />
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136 </tool>