Mercurial > repos > bgruening > deeptools_plot_enrichment

annotate plotEnrichment.xml @ 17:c29ea378c294 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf
author bgruening
date Wed, 20 Feb 2019 09:18:34 -0500
parents c8f8186a479a
children 057ead9b9577
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1 <tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@WRAPPER_VERSION@.0" profile="18.01">
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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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10 @multiple_input_bams@
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11 @BINARY@
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12 @THREADS@
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14 --plotFile '$outFileName'
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16 --bamfiles #echo " ".join($files)#
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17 --labels #echo " ".join($labels)#
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19 @multiple_bed@
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21 #if $outRawCounts:
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22 --outRawCounts '$outFileRawCounts'
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23 #end if
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25 --plotFileFormat '$outFileFormat'
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27 #if str($region).strip() != "":
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28 --region '$region'
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29 #end if
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31 #if $advancedOpt.showAdvancedOpt == "yes"
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32 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
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33 --labels $advancedOpt.labels
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34 #end if
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36 #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
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37 --regionLabels $advancedOpt.regionLabels
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38 #end if
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40 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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41 --plotTitle '$advancedOpt.plotTitle'
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42 #end if
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44 $advancedOpt.perSample
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46 $advancedOpt.variableScales
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48 $advancedOpt.perSample
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50 $advancedOpt.variableScales
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52 --plotWidth '$advancedOpt.plotWidth'
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54 --plotHeight '$advancedOpt.plotHeight'
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56 #if str($advancedOpt.colors).strip() != "":
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57 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
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58 #end if
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60 --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
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62 --alpha '$advancedOpt.alpha'
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64 @ADVANCED_OPTS_READ_PROCESSING@
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65
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66 #if $advancedOpt.Offset:
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67 --Offset $advancedOpt.Offset
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68 #end if
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69
0
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70 @blacklist@
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72 $advancedOpt.keepExons
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74 #end if
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75 ]]>
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76 </command>
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78 <inputs>
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79 <expand macro="multiple_input_bams" MIN="1"/>
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80 <expand macro="custom_sample_labels" />
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81 <expand macro="multiple_bed" />
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83 <expand macro="region_limit_operation" />
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84 <expand macro="input_image_file_format" />
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86 <expand macro="advancedOpt_scaffold">
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87 <param argument="--plotHeight" type="integer" value="20" min="3"
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88 label="Plot height"
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89 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
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91 <param argument="--plotWidth" type="integer" value="20" min="1"
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92 label="Plot width"
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93 help="Width in cm. The default value is 20 centimeters. The minimum value is 1 cm." />
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95 <param argument="--labels" type="text" size="30"
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96 label="Labels for the samples (each BAM file) plotted"
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97 help="The default is to use the file name of the sample. The sample labels should be separated by
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98 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
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99 <sanitizer>
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100 <valid initial="string.printable" />
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101 </sanitizer>
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102 </param>
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103
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104 <param argument="--regionLabels" type="text" size="30"
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105 label="Labels for the features"
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106 help="For BED files, this sets the label for all entries in each file.
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107 For GTF files this is ignored." />
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108
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109 <expand macro="plotTitle" />
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110
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111 <param argument="--alpha" type="float" value="0.9" min="0.0" max="1.0"
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112 label="Alpha channel"
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113 help="The alpha channel value (between 0 and 1). A value of 0 is transparent. Default: 0.9" />
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114
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115 <param argument="--colors" type="text" value="" size="40"
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116 label="List of colors to use for the plotted bars"
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117 help="Color names and html hex strings (e.g. #eeff22) are accepted.
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118 The color names should be separated by spaces. (--colors red blue green)">
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119 <validator type="expression"
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120 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
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121 </param>
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122
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123 <param argument="--perSample" type="boolean" truevalue="--perSample" falsevalue=""
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124 label="Create one plot per-sample"
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125 help="Plot per-sample, rather than per-feature." />
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126
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127 <param argument="--variableScales" type="boolean" truevalue="--variableScales" falsevalue=""
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128 label="Allow variable scales"
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129 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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130
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131 <param argument="--numPlotsPerRow" type="integer" value="4" min="1"
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132 label="Number of plots/row"
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133 help="" />
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134
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135 <expand macro="read_processing_options" />
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136
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137 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
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138 label="Include BED12 exons"
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139 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
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140
6
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141 <param argument="--Offset" type="text" value="" optional="True"
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142 label="Offset inside each alignment to use for the signal location."
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143 help="Uses this offset inside of each read as the signal. This is useful in
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144 cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
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145 should be used to denote where the signal is (rather than the span of the
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146 whole alignment). This can be paired with the --filterRNAstrand option. Note
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147 that negative values indicate offsets from the end of each read. A value of
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148 1 indicates the first base of the alignment (taking alignment orientation
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149 into account). Likewise, a value of -1 is the last base of the alignment. An
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150 offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
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151 used to specify a range of positions. Note that specifying something like
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152 --Offset 5 -1 will result in the 5th through last position being used, which
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153 is equivalent to trimming 4 bases from the 5-prime end of alignments." />
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154
0
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155 <expand macro="blacklist" />
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156
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157 </expand>
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158
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159 <param argument="--outRawCounts" type="boolean" label="Save percentages to a file" help=""/>
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160
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161 </inputs>
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162 <outputs>
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163 <expand macro="output_image_file_format_not_nested" />
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164 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: percentages">
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165 <filter>outRawCounts is True</filter>
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166 </data>
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167 </outputs>
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168 <tests>
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169 <test>
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170 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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171 <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
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172 <param name="outRawCounts" value="true" />
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173 <param name="showAdvancedOpt" value="yes" />
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174 <param name="minMappingQuality" value="0" />
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175 <param name="regionLabels" value="up down" />
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176 <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="1000" />
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177 <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
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178 </test>
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179 </tests>
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180
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181 <help>
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182 <![CDATA[
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183
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184 What it does
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185 -------------
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186
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187 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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188
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189 Output
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190 --------
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191
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192 The output file is a plot in the format specified. A table of the percentages and raw counts can also be created.
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194 .. image:: $PATH_TO_IMAGES/plotEnrichment_output.png
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195 :width: 600
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196 :height: 600
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197
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198 -----
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199
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200 @REFERENCES@
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201 ]]>
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202 </help>
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203 <expand macro="citations" />
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204 </tool>