annotate plotCoverage.xml @ 29:231994413f89 draft default tip

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1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
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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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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 ' '.join(map(str, $BED)) != 'None':
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29 #set bedFileList=[]
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30 #for $f in $BED:
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31 #silent $bedFileList.append("'%s'" % $f)
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32 #end for
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33 #if $bedFileList != ["'None'"]:
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34 --BED #echo ' '.join($bedFileList)#
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35 #end if
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36 #end if
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38 #if $coverageOpt.showCoverageOpt == "yes":
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39 --outCoverageMetrics '$outFileCoverageMetrics'
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40 #for $t in $coverageOpt.thresholds:
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41 -ct $t.coverageThreshold
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42 #end for
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43 #end if
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44
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45 #if $advancedOpt.showAdvancedOpt == "yes":
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46 --numberOfSamples '$advancedOpt.numberOfSamples'
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47 $advancedOpt.skipZeros
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48
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49 #if str($advancedOpt.region).strip() != '':
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50 --region '$advancedOpt.region'
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51 #end if
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52 --numberOfSamples $advancedOpt.numberOfSamples
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53
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54 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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55 --plotTitle '$advancedOpt.plotTitle'
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56 #end if
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57 @ADVANCED_OPTS_READ_PROCESSING@
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58 @PLOTWIDTHHEIGHT@
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59 @blacklist@
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60 #end if
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61
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62 ]]>
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63 </command>
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64 <inputs>
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65
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66 <expand macro="multiple_input_bams" MIN="1"/>
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67 <expand macro="custom_sample_labels" />
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68 <param argument="--BED" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
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69 label="Regions of interest"
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70 help="Limits the coverage analysis to the regions specified in these files. This overrides --numberOfSamples. It is inadvisable to combine this with saving the raw counts." />
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71
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72 <conditional name="coverageOpt">
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73 <param name="showCoverageOpt" type="select" label="Show coverage metrics options">
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74 <option value="no" selected="true">No</option>
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75 <option value="yes">Yes</option>
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76 </param>
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77 <when value="no" />
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78 <when value="yes">
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79 <param argument="--outCoverageMetrics" type="boolean" label="Save per-threshold coverage metrics?"/>
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80 <repeat name="thresholds" title="Coverage Thresholds">
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81 <param argument="--coverageThreshold" type="integer" min="0" label="Coverage Threshold" value="0"/>
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82 </repeat>
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83 </when>
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84 </conditional>
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85
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86 <conditional name="advancedOpt">
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87 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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88 <option value="no" selected="true">No</option>
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89 <option value="yes">Yes</option>
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90 </param>
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91 <when value="no" />
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92 <when value="yes">
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93 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
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94 label="Number of samples"
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95 help="Number of samples taken from the genome to compute the scaling factors."/>
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96 <expand macro="plotWidthHeight" PLOTWIDTH="15.0" PLOTHEIGHT="5.0" />
12
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97 <expand macro="region_limit_operation" />
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98 <expand macro="read_processing_options" />
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99 <expand macro="skipZeros" />
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100 <expand macro="plotTitle" />
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101 <expand macro="blacklist" />
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102 </when>
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103 </conditional>
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104 <expand macro="input_image_file_format" />
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105 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
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106 </inputs>
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107 <outputs>
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108 <expand macro="output_image_file_format_not_nested" />
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109 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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110 <filter>outRawCounts is True</filter>
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111 </data>
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112 <data format="tabular" name="outFileCoverageMetrics" label="${tool.name} on ${on_string}: Threshold Metrics">
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113 <filter>coverageOpt.outCoverageMetrics is True</filter>
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114 </data>
12
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115 </outputs>
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116 <tests>
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117 <test>
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118 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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119 <!--param name="outFileFormat" value="png" /-->
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120 <param name="showAdvancedOpt" value="yes" />
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121 <param name="plotTitle" value="Test Title from Galaxy" />
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122 <param name="outRawCounts" value="True" />
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123 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
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124 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
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125 </test>
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126 <test>
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127 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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128 <param name="showAdvancedOpt" value="yes" />
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129 <param name="plotTitle" value="Test Title from Galaxy" />
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130 <param name="showCoverageOpt" value="yes" />
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131 <param name="coverageThreshold" value="0" />
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132 <param name="coverageThreshold" value="5" />
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133 <param name="coverageThreshold" value="10" />
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134 <param name="coverageThreshold" value="20" />
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135 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
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136 <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" />
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137 </test>
12
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138 </tests>
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139 <help>
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140 <![CDATA[
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141 What it does
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142 -------------
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143
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144 This tool is useful to **assess the sequencing depth** of a given sample.
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145 It samples 1 million bp, counts the number of overlapping reads and reports
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146 a coverage histogram that tells you how many bases are covered how many times.
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147
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148 **Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.
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149
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150 Output
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151 ---------
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152
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153 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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154
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155 The optional output is a table where each row represents the number of reads overlapping with a sampled bp.
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156
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157 .. image:: $PATH_TO_IMAGES/plotCoverage_output.png
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158 :width: 600
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159 :height: 345
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160
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161 Example plot
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162 -----------------
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163
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164 .. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png
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165 :width: 600
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166 :height: 291
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167
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168
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169 @REFERENCES@
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170 ]]>
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171 </help>
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172 <expand macro="citations" />
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173 </tool>