Mercurial > repos > bgruening > deeptools_plot_coverage

annotate plotCoverage.xml @ 24:5ca953cab23b draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
author bgruening
date Fri, 31 Mar 2017 15:55:16 -0400
parents 5f1ab4c4f459
children bed83fb37252
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1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
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2 <description>assesses the sequencing depth of BAM files </description>
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3 <macros>
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4 <token name="@BINARY@">plotCoverage</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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15 @BINARY@
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17 @THREADS@
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18
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19 --plotFile '$outFileName'
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20 --bamfiles #echo " ".join($files)#
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21 --labels #echo " ".join($labels)#
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22 --plotFileFormat "$outFileFormat"
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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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27
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28 #if $advancedOpt.showAdvancedOpt == "yes":
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29 --numberOfSamples '$advancedOpt.numberOfSamples'
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30 $advancedOpt.skipZeros
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31
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32 #if str($advancedOpt.region).strip() != '':
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33 --region '$advancedOpt.region'
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34 #end if
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35 --numberOfSamples $advancedOpt.numberOfSamples
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36
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37 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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38 --plotTitle '$advancedOpt.plotTitle'
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39 #end if
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40 @ADVANCED_OPTS_READ_PROCESSING@
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41 @blacklist@
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42 #end if
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43
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44 ]]>
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45 </command>
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46 <inputs>
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47
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48 <expand macro="multiple_input_bams" />
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49
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50 <conditional name="advancedOpt">
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51 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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52 <option value="no" selected="true">no</option>
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53 <option value="yes">yes</option>
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54 </param>
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55 <when value="no" />
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56 <when value="yes">
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57 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
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58 label="Number of samples"
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59 help="Number of samples taken from the genome to compute the scaling factors."/>
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60 <expand macro="region_limit_operation" />
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61 <expand macro="read_processing_options" />
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62 <expand macro="skipZeros" />
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63 <expand macro="plotTitle" />
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64 <expand macro="blacklist" />
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65 </when>
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66 </conditional>
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67
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68 <expand macro="input_image_file_format" />
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69 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
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70
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71
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72 </inputs>
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73 <outputs>
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74 <expand macro="output_image_file_format_not_nested" />
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75 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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76 <filter>outRawCounts is True</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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82 <!--param name="outFileFormat" value="png" /-->
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83 <param name="showAdvancedOpt" value="yes" />
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84 <param name="plotTitle" value="Test Title from Galaxy" />
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85 <param name="outRawCounts" value="True" />
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86 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
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87 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
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88 </test>
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89 </tests>
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90 <help>
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91 <![CDATA[
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92 What it does
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93 -------------
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94
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95 This tool is useful to **assess the sequencing depth** of a given sample.
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96 It samples 1 million bp, counts the number of overlapping reads and reports
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97 a coverage histogram that tells you how many bases are covered how many times.
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98
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99 **Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.
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100
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101 Output
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102 ---------
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103
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104 The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more.
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105
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106 The optional output is a table where each row represents the number of reads overlapping with a sampled bp.
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107
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108 .. image:: $PATH_TO_IMAGES/plotCoverage_output.png
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109 :width: 600
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110 :height: 345
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111
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112 Example plot
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113 -----------------
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114
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115 .. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png
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116 :width: 600
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117 :height: 291
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118
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119
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120 @REFERENCES@
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121 ]]>
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122 </help>
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123 <expand macro="citations" />
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124 </tool>