Mercurial > repos > bgruening > deeptools_multi_bam_summary

annotate multiBamSummary.xml @ 14:3a8cfc0d5706 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
author bgruening
date Sun, 14 May 2017 18:12:45 -0400
parents d0800b8adbcb
children d564cdad7638
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1 <tool id="deeptools_multi_bam_summary" name="multiBamSummary" version="@WRAPPER_VERSION@.0">
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2 <description>calculates average read coverages for a list of two or more BAM files</description>
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3 <macros>
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4 <token name="@BINARY@">multiBamSummary</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_bams@
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14 @BINARY@
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15 $mode.modeOpt
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16 @THREADS@
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18 --outFileName '$outFile'
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19 --bamfiles #echo " ".join($files)#
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20 --labels #echo " ".join($labels)#
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22 #if $outRawCounts:
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23 --outRawCounts '$outFileRawCounts'
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24 #end if
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26 #if $mode.modeOpt == "bins":
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27 --binSize '$mode.binSize'
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28 --distanceBetweenBins '$mode.distanceBetweenBins'
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29 #else:
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30 --BED $mode.region_file
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31 #end if
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33 #if str($region).strip() != '':
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34 --region '$region'
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35 #end if
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37 #if $advancedOpt.showAdvancedOpt == "yes":
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38 @ADVANCED_OPTS_READ_PROCESSING@
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39 @ADVANCED_OPTS_GTF@
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40 @blacklist@
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41 #end if
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42 ]]>
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43 </command>
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44
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45 <inputs>
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46 <expand macro="multiple_input_bams" MIN="2"/>
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47
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48 <conditional name="mode">
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49 <param name="modeOpt" type="select" label="Choose computation mode"
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50 help="In the bins mode, the coverage is computed for equally
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51 sized bins. \nIn BED file mode, a list of genomic regions
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52 in BED or INTERVAL format has to be given. For each region
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53 in the BED file, the number of overlapping reads from each BAM file is counted.
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54 ">
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55 <option value="bins" selected="true">Bins</option>
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56 <option value="BED-file">Limit calculation to certain regions (BED file)</option>
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57 </param>
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58 <when value="bins">
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59 <param name="binSize" type="integer" value="10000" min="1"
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60 label="Bin size in bp"
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61 help="Length in bases of the window used to sample the genome. (--binSize)"/>
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62
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63 <expand macro="distanceBetweenBins" />
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64
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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 or INTERVAL format"
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69 help="Coverage 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
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75 <expand macro="advancedOpt_scaffold">
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76 <expand macro="read_processing_options" />
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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 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
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82
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83 </inputs>
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84 <outputs>
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85 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
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86 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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87 <filter>outRawCounts is True</filter>
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88 </data>
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89 </outputs>
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90 <tests>
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91 <test>
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92 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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93 <param name="modeOpt" value="bins" />
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94 <param name="binSize" value="10" />
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95 <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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96 </test>
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97 <test>
6
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98 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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99 <param name="modeOpt" value="BED-file" />
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100 <param name="region_file" value="multiBamSummary_regions.bed" />
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101 <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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102 </test>
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103
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104
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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 -------------
0
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111
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112 This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files).
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113 The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted.
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114 Alternatively, an interval file with pre-defined genomic regions can be provided.
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115
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116 In principle, this tool does the same as ``multiBigwigSummary``, but for BAM files.
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117
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118 A typical follow-up application is to check and visualize the similarity and variability between replicates or published data sets (see: ``plotPCA`` and ``plotCorrelation``).
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119
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120 Output
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121 --------
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122
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123 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``.
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124
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125 To analyze the coverage 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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126
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127 .. image:: $PATH_TO_IMAGES/multiBamSummary_output.png
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128 :width: 600
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129 :height: 443
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130
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131 -----
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132
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133 @REFERENCES@
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134 ]]>
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135 </help>
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136 <expand macro="citations" />
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137 </tool>