Mercurial > repos > bgruening > deeptools_plot_enrichment

annotate plotEnrichment.xml @ 0:c53dcf458fc0 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
author bgruening
date Thu, 11 Aug 2016 06:30:10 -0400
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c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
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1 <tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@WRAPPER_VERSION@.0">
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2 <description>plots read/fragment coverage over sets of regions</description>
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3 <macros>
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4 <token name="@BINARY@">plotEnrichment</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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11 @multiple_input_bams@
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12 @BINARY@
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13 @THREADS@
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15 --plotFile '$outFileName'
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17 --bamfiles #echo " ".join($files)#
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18 --labels #echo " ".join($labels)#
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20 @multiple_bed@
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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 --plotFileFormat "$outFileFormat"
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27
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28 #if str($region).strip() != "":
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29 --region '$region'
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30 #end if
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32 #if $advancedOpt.showAdvancedOpt == "yes"
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33 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
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34 --labels $advancedOpt.labels
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35 #end if
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37 #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
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38 --regionLabels $advancedOpt.regionLabels
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39 #end if
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41 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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42 --plotTitle '$advancedOpt.plotTitle'
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43 #end if
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44
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45 $advancedOpt.perSample
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46
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47 $advancedOpt.variableScales
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49 $advancedOpt.perSample
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51 $advancedOpt.variableScales
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53 --plotWidth '$advancedOpt.plotWidth'
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54
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55 --plotHeight '$advancedOpt.plotHeight'
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56
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57 #if str($advancedOpt.colors).strip() != "":
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58 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
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59 #end if
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60
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61 --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
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62
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63 --alpha '$advancedOpt.alpha'
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64
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65 @ADVANCED_OPTS_READ_PROCESSING@
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66
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67 @blacklist@
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68
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69 $advancedOpt.keepExons
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70
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71 #end if
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72 ]]>
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73 </command>
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74
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75 <inputs>
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76 <expand macro="multiple_input_bams" />
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77 <expand macro="multiple_bed" />
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78
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79 <expand macro="region_limit_operation" />
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80 <expand macro="input_image_file_format" />
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81
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82 <expand macro="advancedOpt_scaffold">
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83 <param argument="--plotHeight" type="integer" value="20" min="3"
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84 label="Plot height"
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85 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
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86
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87 <param argument="--plotWidth" type="integer" value="20" min="1"
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88 label="Plot width"
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89 help="Width in cm. The default value is 20 centimeters. The minimum value is 1 cm." />
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90
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91 <param argument="--labels" type="text" size="30"
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92 label="Labels for the samples (each BAM file) plotted"
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93 help="The default is to use the file name of the sample. The sample labels should be separated by
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94 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
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95 <sanitizer>
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96 <valid initial="string.printable" />
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97 </sanitizer>
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98 </param>
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99
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100 <param argument="--regionLabels" type="text" size="30"
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101 label="Labels for the features"
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102 help="For BED files, this sets the label for all entries in each file.
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103 For GTF files this is ignored." />
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104
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105 <expand macro="plotTitle" />
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106
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107 <param argument="--alpha" type="float" value="0.9" min="0.0" max="1.0"
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108 label="Alpha channel"
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109 help="The alpha channel value (between 0 and 1). A value of 0 is transparent. Default: 0.9" />
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110
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111 <param argument="--colors" type="text" value="" size="40"
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112 label="List of colors to use for the plotted bars"
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113 help="Color names and html hex strings (e.g. #eeff22) are accepted.
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114 The color names should be separated by spaces. (--colors red blue green)">
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115 <validator type="expression"
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116 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
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117 </param>
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118
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119 <param argument="--perSample" type="boolean" truevalue="--perSample" falsevalue=""
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120 label="Create one plot per-sample"
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121 help="Plot per-sample, rather than per-feature." />
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122
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123 <param argument="--variableScales" type="boolean" truevalue="--variableScales" falsevalue=""
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124 label="Allow variable scales"
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125 help="By default, the y-axis always goes from 0 to 100. If this option is selected, then the maximum value will vary with the dataset." />
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126
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127 <param argument="--numPlotsPerRow" type="integer" value="4" min="1"
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128 label="Number of plots/row"
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129 help="" />
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130
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131 <expand macro="read_processing_options" />
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132
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133 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
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134 label="Include BED12 exons"
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135 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
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136
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137 <expand macro="blacklist" />
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138
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139 </expand>
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140
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141 <param argument="--outRawCounts" type="boolean" label="Save percentages to a file" help=""/>
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142
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143 </inputs>
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144 <outputs>
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145 <expand macro="output_image_file_format_not_nested" />
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146 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: percentages">
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147 <filter>outRawCounts is True</filter>
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148 </data>
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149 </outputs>
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150 <tests>
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151 <test>
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152 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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153 <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
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154 <param name="outRawCounts" value="true" />
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155 <param name="showAdvancedOpt" value="yes" />
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156 <param name="minMappingQuality" value="0" />
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157 <param name="regionLabels" value="up down" />
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158 <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="1000" />
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159 <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
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160 </test>
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161 </tests>
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162
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163 <help>
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164 <![CDATA[
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165
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166 What it does
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167 -------------
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168
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169 This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed.
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170
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171 Output
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172 --------
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173
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174 The output file is a plot in the format specified. A table of the percentages can also be created.
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175
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176 .. image:: $PATH_TO_IMAGES/plotEnrichment_output.png
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177 :width: 600
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178 :height: 600
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179
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180 -----
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181
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182 @REFERENCES@
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183 ]]>
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184 </help>
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185 <expand macro="citations" />
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186 </tool>