Mercurial > repos > bgruening > deeptools_multi_bam_coverage

annotate multiBamCoverage.xml @ 0:c6136c6011fd draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
author bgruening
date Tue, 19 Jan 2016 10:04:43 -0500
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0
c6136c6011fd planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
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1 <tool id="deeptools_multi_bam_coverage" name="multiBamCoverage" 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@">multiBamCoverage</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 $mode.modeOpt
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16 @THREADS@
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17
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18 --outFileName '$outFile'
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19 --bamfiles '#echo "' '".join($files)#'
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20 --labels '#echo "' '".join($labels)#'
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21
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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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25
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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 $mode.region_file
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31 #end if
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32
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33 #if str($region).strip() != '':
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34 --region '$region'
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35 #end if
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36
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37 #if $advancedOpt.showAdvancedOpt == "yes":
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38 @ADVANCED_OPTS_READ_PROCESSING@
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39 #end if
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40 ]]>
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41 </command>
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42
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43 <inputs>
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44 <expand macro="multiple_input_bams" />
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45
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46 <conditional name="mode">
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47 <param name="modeOpt" type="select" label="Choose computation mode"
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48 help="In the bins mode, the coverage is computed for equally
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49 sized bins. In the BED file mode, a list of genomic regions in BED
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50 format has to be given. For each region in the BED file the number of
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51 overlapping reads is counted in each of the BAM files.
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52 ">
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53 <option value="bins" selected="true">Bins</option>
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54 <option value="BED-file">Limit calculation to certain regions (BED file)</option>
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55 </param>
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56 <when value="bins">
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57 <param name="binSize" type="integer" value="10000" min="1"
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58 label="Bin size in bp"
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59 help="Length in bases of the window used to sample the genome. (--binSize)"/>
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60
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61 <expand macro="distanceBetweenBins" />
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62
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63 </when>
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64 <when value="BED-file">
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65 <param name="region_file" type="data" format="bed"
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66 label="Region file in BED format"
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67 help="Coverage is computed for the number of reads that overlap such regions."/>
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68 </when>
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69 </conditional>
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70
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71 <expand macro="region_limit_operation" />
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72
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73 <expand macro="advancedOpt_scaffold">
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74 <expand macro="read_processing_options" />
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75 </expand>
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76
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77 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
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78
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79 </inputs>
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80 <outputs>
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81 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
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82 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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83 <filter>outRawCounts is True</filter>
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84 </data>
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85 </outputs>
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86 <tests>
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87 <test>
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88 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
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89 <param name="modeOpt" value="bins" />
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90 <param name="binSize" value="10" />
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91 <output name="outFile" file="multiBamCoverage_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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92 </test>
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93 <test>
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94 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
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95 <param name="modeOpt" value="BED-file" />
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96 <param name="region_file" value="multiBamCoverage_regions.bed" />
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97 <output name="outFile" file="multiBamCoverage_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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98 </test>
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99
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100
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101 </tests>
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102 <help>
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103 <![CDATA[
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104
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105 **What it does**
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106
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107 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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108 The genome is split into bins of the given size. For each bin, the number of reads found in it in each BAM file is counted.
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109 Alternatively, a bed file with pre-defined genomic regions can be provided. In each case the calculation can further be limited to
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110 a given genomic interval (e.g. a given chromosome). This option is mostly used for testing and efficiency.
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111 A typical follow-up application is to check and visualize the similarity between replicates or published data sets (see: plotPCA and plotCorrelation).
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112
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113 **Output files**:
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114
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115 - **score matrix**: a compressed matrix where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file)
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116 - Optional : Uncompressed **score matrix**, in case you want to analyse the coverage scores yourself. (Select to "Save raw counts" from above)
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117
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118 =======
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119
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120 .. image:: $PATH_TO_IMAGES/QC_multiBamCoverage_humanSamples.png
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121 :alt: Heatmap of RNA Polymerase II ChIP-seq
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122
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123
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124 You can find more details on the multiBamCoverage doc page: https://deeptools.readthedocs.org/en/master/content/tools/multiBamCoverage.html
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125
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126 -----
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127
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128 @REFERENCES@
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129 ]]>
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130 </help>
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131 <expand macro="citations" />
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132 </tool>