Mercurial > repos > bgruening > deeptools

annotate profiler.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children
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f7712a057440 new bugfix release
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1 <tool id="deeptools_profiler" name="profiler" version="@WRAPPER_VERSION@.0">
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2 <description>
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3 creates a profile plot for a score associated to genomic regions
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4 </description>
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5 <macros>
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6 <token name="@BINARY@">profiler</token>
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7 <import>deepTools_macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <command>
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11 <![CDATA[
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12 profiler
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13
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14 --matrixFile $matrixFile
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15 --outFileName $outFileName
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16
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17 #if $output.showOutputSettings == "yes"
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18 --plotFileFormat $output.outFileFormat
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19
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20 #if $output.saveData:
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21 --outFileNameData '$outFileNameData'
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22 #end if
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23
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24 #if $output.saveSortedRegions:
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25 --outFileSortedRegions '$outFileSortedRegions'
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26 #end if
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27 #else
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28 --plotFileFormat 'png'
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29 #end if
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30
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31 #if $scaleRegions.showScaleRegionsOpt == "yes":
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32 --startLabel '$scaleRegions.startLabel'
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33 --endLabel '$scaleRegions.endLabel'
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34 #end if
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35
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36 #if $advancedOpt.showAdvancedOpt == "yes":
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37 #if $advancedOpt.averageType:
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38 --averageType '$advancedOpt.averageType'
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39 #end if
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40 --plotHeight $advancedOpt.plotHeight
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41 --plotWidth $advancedOpt.plotWidth
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42 --plotType $advancedOpt.plotType
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43
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44 --regionsLabel '$advancedOpt.regionsLabel'
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45
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46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
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47 --plotTitle '$advancedOpt.plotTitle'
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48 #end if
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49
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50 #if str($advancedOpt.colors).strip() != "":
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51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
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52 #end if
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53
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54 $advancedOpt.onePlotPerGroup
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55
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56 #if $advancedOpt.yMin:
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57 --yMin $advancedOpt.yMin
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58 #end if
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59 #if $advancedOpt.yMax:
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60 --yMax $advancedOpt.yMax
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61 #end if
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62
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63 --xAxisLabel '$advancedOpt.xAxisLabel'
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64 #if str($advancedOpt.yAxisLabel.value) != "None":
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65 --yAxisLabel '$advancedOpt.yAxisLabel'
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66 #end if
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67
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68 @KMEANS_CLUSTERING@
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69
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70 #end if
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71 ]]>
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72 </command>
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73 <inputs>
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74 <param name="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
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75 <conditional name="scaleRegions">
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76 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
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77 <option value="no" selected="true">no</option>
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78 <option value="yes">yes</option>
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79 </param>
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80 <when value="no" />
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81 <when value="yes">
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82 <param name="startLabel" type="text" value="TSS" size="10"
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83 label="Label for the region start"
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84 help ="[only for scale-regions mode] Label shown in the plot
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85 for the start of the region. Default is TSS (transcription start site),
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86 but could be changed to anything, e.g. &quot;peak start&quot;." />
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87 <param name="endLabel" type="text" value="TES" size="10"
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88 label="Label for the region end"
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89 help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
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90 </when>
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91 </conditional>
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92
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93 <expand macro="input_graphic_output_settings">
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94 <expand macro="input_image_file_format" />
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95 </expand>
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96
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97 <conditional name="advancedOpt">
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98 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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99 <option value="no" selected="true">no</option>
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100 <option value="yes">yes</option>
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101 </param>
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102 <when value="no" />
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103 <when value="yes">
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104 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
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105 <option value="mean" selected="true">mean</option>
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106 <option value="median">median</option>
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107 <option value="min">min</option>
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108 <option value="max">max</option>
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109 <option value="sum">sum</option>
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110 <option value="std">std</option>
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111 </param>
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112 <param name="plotHeight" type="integer" value="5" min="3"
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113 label="Plot height"
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114 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
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115 <param name="plotWidth" type="integer" value="8" min="1"
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116 label="Plot width"
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117 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
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118 <param name="plotType" type="select" label="Plot type"
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119 help="For the summary plot (profile) only. The &quot;lines&quot; option will
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120 plot the profile line based on the average type selected. The &quot;fill&quot;
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121 option fills the region between zero and the profile curve. The fill in color is
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122 semi transparent to distinguish different profiles. The &quot;add standard error&quot;
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123 option colors the region between the profile and the standard error of the data.
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124 As in the case of fill, a semi-transparent color is used.
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125 The option &quot;overlapped_lines&quot; plots each region values, one on top of
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126 the other; this option only works if &quot;one plot per proup&quot; is set.">
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127 <option value="lines" selected="true">lines</option>
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128 <option value="fill">fill</option>
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129 <option value="se">add standard error</option>
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130 <option value="overlapped_lines">overlapped lines</option>
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131 </param>
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132 <param name="regionsLabel" type="text" value="genes" size="30"
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133 label="Labels for the regions plotted in the heatmap"
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134 help="If more than one region is being plotted a list of labels separated
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135 by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
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136
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137 <expand macro="plotTitle" />
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138 <param name="colors" type="text" value="" size="40"
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139 label="List of colors to use for the plotted lines"
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140 help="Color names and html hex strings (e.g. #eeff22) are accepted.
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141 The color names should be given separated by spaces. (--colors red blue green)">
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142 <validator type="expression"
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143 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
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144 </param>
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145
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146 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
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147 label="Do one plot per group"
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148 help="When the region file contains groups separated by &quot;#&quot;, the default is
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149 to plot the averages for the distinct plots in one plot. If this option is set, each group
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150 will get its own plot, stacked on top of each other."/>
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151 <param name="yMin" type="float" value="" size="3" optional="true"
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152 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
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153 <param name="yMax" type="float" value="" size="3" optional="true"
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154 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
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155 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50"
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156 label="Description for the x-axis label" />
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157 <param name="yAxisLabel" type="text" value="" size="50"
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158 label="Description for the y-axis label for the top panel" />
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159
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160 <expand macro="kmeans_clustering" />
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161
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162 </when>
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163 </conditional>
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164 </inputs>
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165 <outputs>
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166 <expand macro="output_image_file_format" />
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167 <expand macro="output_graphic_outputs" />
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168 </outputs>
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169 <tests>
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170 <test>
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171 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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172 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" />
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173 </test>
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174 </tests>
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175 <help>
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176 <![CDATA[
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177
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178 **What it does**
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179
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180 This tool plots the average enrichments over all genomic
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181 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
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182 It is a very useful complement to the heatmapper, especially in cases when you want to
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183 compare the scores for many different groups. Like heatmapper, profiler does not change the
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184 values that were compute by computeMatrix, but you can choose between
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185 many different ways to color and display the plots.
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186
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187
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188 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
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189 :alt: Meta-gene profile of Rna Polymerase II
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190
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191
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192 You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
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193
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194
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195 -----
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196
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197 @REFERENCES@
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198 ]]>
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199 </help>
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200 <expand macro="citations" />
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201 </tool>