annotate heatmapper.xml @ 30:5231f398d784 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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date Tue, 20 Oct 2015 14:43:12 -0400
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1 <tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0">
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2 <description>creates a heatmap for a score associated to genomic regions</description>
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3 <macros>
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4 <token name="@BINARY@">heatmapper</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 heatmapper
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11
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12 --matrixFile $matrixFile
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13 --outFileName $outFileName
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14
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15 #if $output.showOutputSettings == "yes"
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16 --plotFileFormat $output.outFileFormat
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17 #if $outFileNameData:
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18 --outFileNameData '$outFileNameData'
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19 #end if
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20
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21 #if $outFileNameMatrix:
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22 --outFileNameMatrix '$outFileNameMatrix'
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23 #end if
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24
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25 #if $outFileSortedRegions:
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26 --outFileSortedRegions '$outFileSortedRegions'
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27 #end if
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28 #else
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29 --plotFileFormat 'png'
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30 #end if
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31
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32 #if $advancedOpt.showAdvancedOpt == "yes"
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33 #if $advancedOpt.sortRegions:
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34 --sortRegions '$advancedOpt.sortRegions'
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35 #end if
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36
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37 #if $advancedOpt.sortUsing:
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38 --sortUsing '$advancedOpt.sortUsing'
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39 #end if
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40
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41 #if $advancedOpt.averageTypeSummaryPlot:
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42 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
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43 #end if
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44
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45 #if str($advancedOpt.missingDataColor.value) != "None":
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46 --missingDataColor '$advancedOpt.missingDataColor'
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47 #end if
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48
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49 --colorMap '$advancedOpt.colorMap'
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50
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51 #if str($advancedOpt.zMin).strip() != "":
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52 --zMin $advancedOpt.zMin
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53 #end if
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54 #if $advancedOpt.zMax:
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55 --zMax $advancedOpt.zMax
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56 #end if
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57
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58 #if str($advancedOpt.yMin).strip() != "":
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59 --yMin $advancedOpt.yMin
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60 #end if
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61 #if $advancedOpt.yMax:
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62 --yMax $advancedOpt.yMax
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63 #end if
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64
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65 --xAxisLabel '$advancedOpt.xAxisLabel'
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66 --yAxisLabel '$advancedOpt.yAxisLabel'
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67
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68 --heatmapWidth $advancedOpt.heatmapWidth
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69 --heatmapHeight $advancedOpt.heatmapHeight
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70
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71 --whatToShow '$advancedOpt.whatToShow'
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72
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73 --startLabel '$advancedOpt.startLabel'
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74 --endLabel '$advancedOpt.endLabel'
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75 --refPointLabel '$advancedOpt.referencePointLabel'
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76 --regionsLabel '$advancedOpt.regionsLabel'
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77
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78 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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79 --plotTitle '$advancedOpt.plotTitle'
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80 #end if
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81
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82 $advancedOpt.onePlotPerGroup
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83
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84 @KMEANS_CLUSTERING@
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85
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86 #end if
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87 ]]>
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88 </command>
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89 <inputs>
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90 <param name="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
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91
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92 <expand macro="input_graphic_output_settings">
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93 <expand macro="input_image_file_format" />
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94 <expand macro="input_save_matrix_values" />
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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="sortRegions" type="select" label="Sort regions"
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105 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region. (--sortRegions)">
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106 <option value="no">no ordering</option>
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107 <option value="descend" selected="true">descending order</option>
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108 <option value="ascend">ascending order</option>
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109 </param>
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110
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111 <param name="sortUsing" type="select" label="Method used for sorting"
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112 help="For each row the method is computed. (--sortUsing)">
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113 <option value="mean" selected="true">mean</option>
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114 <option value="median">median</option>
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115 <option value="min">min</option>
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116 <option value="max">max</option>
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117 <option value="sum">sum</option>
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118 <option value="region_length">region length</option>
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119 </param>
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120
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121 <param name="averageTypeSummaryPlot" type="select"
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122 label="Type of statistic that should be plotted in the summary image above the heatmap"
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123 help="(--averageTypeSummaryPlot)">
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124 <option value="mean" selected="true">mean</option>
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125 <option value="median">median</option>
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126 <option value="min">min</option>
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127 <option value="max">max</option>
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128 <option value="sum">sum</option>
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129 <option value="std">std</option>
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130 </param>
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131
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132 <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color"
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133 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
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134 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
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135 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
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136 Alternatively colors can be specified using the #rrggbb notation. (--missingDataColor)" />
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137
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138 <expand macro="colormap" />
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139
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140 <param name="zMin" type="float" value="" size="3"
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141 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help="(--zMin)"/>
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142 <param name="zMax" type="float" value="" size="3"
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143 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help="(--zMax)"/>
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144 <param name="yMin" type="float" value="" size="3"
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145 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help="(--yMin)"/>
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146 <param name="yMax" type="float" value="" size="3"
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147 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help="(--yMax)"/>
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148 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
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149 label="Description for the x-axis label" help="(--xAxisLabel)"/>
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150 <param name="yAxisLabel" type="text" value="genes" size="30"
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151 label="Description for the y-axis label for the top panel" help="(--yAxisLabel)"/>
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152
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153 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100"
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154 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
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155 <param name="heatmapHeight" type="float" value="25" min="3" max="100"
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156 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
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157
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158 <param name="whatToShow" type="select" label="What to show"
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159 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar. (--whatToShow)">
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160 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
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161 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
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162 <option value="heatmap only">heatmap only</option>
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163 <option value="heatmap and colorbar">heatmap and colorbar</option>
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164 <option value="colorbar only">colorbar only</option>
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165 </param>
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166
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167 <param name="startLabel" type="text" value="TSS" size="10"
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168 label="Label for the region start"
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169 help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;. (--startLabel)" />
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170 <param name="endLabel" type="text" value="TES" size="10"
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171 label="Label for the region end"
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172 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/>
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173
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174 <param name="referencePointLabel" type="text" value="TSS" size="10"
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175 label="Reference point label"
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176 help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc. (--referencePointLabel)" />
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177 <param name="regionsLabel" type="text" value="genes" size="30"
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178 label="Labels for the regions plotted in the heatmap"
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179 help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2. (--regionsLabel)">
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180 <sanitizer>
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181 <valid initial="string.printable">
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182 </valid>
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183 </sanitizer>
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184 </param>
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185 <expand macro="plotTitle" />
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186 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
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187 label="Do one plot per group"
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188 help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default.
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189 If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/>
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190
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191 <expand macro="kmeans_clustering" />
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192 </when>
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193 </conditional>
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194 </inputs>
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195 <outputs>
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196 <expand macro="output_image_file_format" />
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197 <expand macro="output_graphic_outputs" />
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198 <expand macro="output_save_matrix_values" />
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199 </outputs>
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200 <tests>
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201 <test>
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202 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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203 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
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204 </test>
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205 </tests>
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206 <help>
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207 <![CDATA[
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208 **What it does**
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209
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210 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
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211 Like profiler, it requires that computeMatrix was run first to calculate the values.
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212
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213 We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as
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214 with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of
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215 groups with similar read distributions that you expect and the algorithm will do the sorting for you.
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216
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217 Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
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218
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219
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220 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
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221 :alt: Heatmap of RNA Polymerase II ChIP-seq
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222
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223
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224 You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
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225
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226
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227 -----
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228
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229 @REFERENCES@
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230 ]]>
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231 </help>
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232 <expand macro="citations" />
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233 </tool>