Mercurial > repos > bgruening > deeptools_plot_coverage

annotate plotCoverage.xml @ 22:3a539cb281ba draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
author bgruening
date Tue, 19 Feb 2019 09:59:04 -0500
parents 7373bed2be0f
children 4e12ea27f788
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1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0" profile="18.01">
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2 <description>assesses the sequencing depth of BAM/CRAM 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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13 @multiple_input_bams@
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15 @BINARY@
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17 @THREADS@
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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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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 @PLOTWIDTHHEIGHT@
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42 @blacklist@
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43 #end if
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45 ]]>
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46 </command>
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47 <inputs>
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48
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49 <expand macro="multiple_input_bams" MIN="1"/>
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50 <expand macro="custom_sample_labels" />
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51
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52 <conditional name="advancedOpt">
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53 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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54 <option value="no" selected="true">no</option>
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55 <option value="yes">yes</option>
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56 </param>
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57 <when value="no" />
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58 <when value="yes">
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59 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
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60 label="Number of samples"
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61 help="Number of samples taken from the genome to compute the scaling factors."/>
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62 <expand macro="plotWidthHeight" PLOTWIDTH="15.0" PLOTHEIGHT="5.0" />
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63 <expand macro="region_limit_operation" />
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64 <expand macro="read_processing_options" />
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65 <expand macro="skipZeros" />
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66 <expand macro="plotTitle" />
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67 <expand macro="blacklist" />
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68 </when>
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69 </conditional>
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70
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71 <expand macro="input_image_file_format" />
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72 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
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73
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74
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75 </inputs>
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76 <outputs>
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77 <expand macro="output_image_file_format_not_nested" />
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78 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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79 <filter>outRawCounts is True</filter>
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80 </data>
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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85 <!--param name="outFileFormat" value="png" /-->
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86 <param name="showAdvancedOpt" value="yes" />
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87 <param name="plotTitle" value="Test Title from Galaxy" />
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88 <param name="outRawCounts" value="True" />
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89 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
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90 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
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91 </test>
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92 </tests>
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93 <help>
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94 <![CDATA[
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95 What it does
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96 -------------
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97
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98 This tool is useful to **assess the sequencing depth** of a given sample.
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99 It samples 1 million bp, counts the number of overlapping reads and reports
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100 a coverage histogram that tells you how many bases are covered how many times.
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101
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102 **Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.
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103
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104 Output
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105 ---------
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106
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107 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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108
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109 The optional output is a table where each row represents the number of reads overlapping with a sampled bp.
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110
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111 .. image:: $PATH_TO_IMAGES/plotCoverage_output.png
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112 :width: 600
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113 :height: 345
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114
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115 Example plot
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116 -----------------
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117
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118 .. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png
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119 :width: 600
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120 :height: 291
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121
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122
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123 @REFERENCES@
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124 ]]>
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125 </help>
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126 <expand macro="citations" />
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127 </tool>