Mercurial > repos > bgruening > deeptools_plot_heatmap
annotate plotHeatmap.xml @ 0:e1bb51933e7f draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author | bgruening |
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date | Mon, 25 Jan 2016 20:16:56 -0500 |
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children | 6a247ae015cc |
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0
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0"> |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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2 <description>creates a heatmap for a score associated to genomic regions</description> |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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3 <macros> |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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4 <token name="@BINARY@">plotHeatmap</token> |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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5 <import>deepTools_macros.xml</import> |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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6 </macros> |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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7 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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8 <command> |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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9 <![CDATA[ |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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10 @BINARY@ |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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11 --matrixFile "$matrixFile" |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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12 --outFileName "$outFileName" |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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13 |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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14 #if $output.showOutputSettings == "yes" |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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15 --plotFileFormat "$output.outFileFormat" |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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16 |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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17 #if $outFileNameMatrix: |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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18 --outFileNameMatrix "$outFileNameMatrix" |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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19 #end if |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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20 |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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21 #if $outFileSortedRegions: |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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22 --outFileSortedRegions "$outFileSortedRegions" |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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23 #end if |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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24 #else |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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25 --plotFileFormat 'png' |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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26 #end if |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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27 |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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28 #if $advancedOpt.showAdvancedOpt == "yes" |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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29 #if $advancedOpt.sortRegions: |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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30 --sortRegions '$advancedOpt.sortRegions' |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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31 #end if |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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32 |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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33 #if $advancedOpt.sortUsing: |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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34 --sortUsing '$advancedOpt.sortUsing' |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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35 #end if |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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36 |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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37 #if $advancedOpt.averageTypeSummaryPlot: |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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38 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot' |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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39 #end if |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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40 |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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41 #if str($advancedOpt.missingDataColor.value) != "None": |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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42 --missingDataColor '$advancedOpt.missingDataColor' |
e1bb51933e7f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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43 #end if |
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44 |
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45 --colorMap '$advancedOpt.colorMap' |
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46 |
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47 #if str($advancedOpt.zMin).strip() != "": |
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48 --zMin $advancedOpt.zMin |
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49 #end if |
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50 #if $advancedOpt.zMax: |
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51 --zMax $advancedOpt.zMax |
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52 #end if |
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53 |
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54 #if str($advancedOpt.yMin).strip() != "": |
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55 --yMin $advancedOpt.yMin |
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56 #end if |
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57 #if $advancedOpt.yMax: |
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58 --yMax $advancedOpt.yMax |
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59 #end if |
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60 |
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61 --xAxisLabel '$advancedOpt.xAxisLabel' |
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62 --yAxisLabel '$advancedOpt.yAxisLabel' |
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63 |
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64 --heatmapWidth $advancedOpt.heatmapWidth |
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65 --heatmapHeight $advancedOpt.heatmapHeight |
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66 |
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67 --whatToShow '$advancedOpt.whatToShow' |
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68 |
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69 --startLabel '$advancedOpt.startLabel' |
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70 --endLabel '$advancedOpt.endLabel' |
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71 --refPointLabel '$advancedOpt.referencePointLabel' |
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72 --regionsLabel '$advancedOpt.regionsLabel' |
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73 |
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74 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": |
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75 --plotTitle '$advancedOpt.plotTitle' |
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76 #end if |
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77 |
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78 $advancedOpt.perGroup |
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79 |
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80 @KMEANS_CLUSTERING@ |
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81 |
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82 #end if |
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83 ]]> |
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84 </command> |
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85 <inputs> |
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86 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/> |
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87 |
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88 <expand macro="input_graphic_output_settings"> |
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89 <expand macro="input_image_file_format" /> |
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90 <expand macro="input_save_matrix_values" /> |
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91 </expand> |
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92 |
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93 <conditional name="advancedOpt" > |
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94 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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95 <option value="no" selected="true">no</option> |
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96 <option value="yes">yes</option> |
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97 </param> |
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98 <when value="no" /> |
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99 <when value="yes"> |
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100 <expand macro="sortRegions" /> |
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101 <expand macro="sortUsing" /> |
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102 <param argument="--averageTypeSummaryPlot" type="select" |
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103 label="Type of statistic that should be plotted in the summary image above the heatmap" |
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104 help=""> |
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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 |
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113 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" |
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114 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. |
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115 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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116 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. |
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117 Alternatively colors can be specified using the #rrggbb notation." /> |
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118 |
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119 <expand macro="colorMap" /> |
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120 |
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121 <param argument="--zMin" type="float" value="" size="3" optional="True" |
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122 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/> |
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123 <param argument="--zMax" type="float" value="" size="3" optional="True" |
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124 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/> |
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125 <param argument="--yMin" type="float" value="" size="3" optional="True" |
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126 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/> |
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127 <param argument="--yMax" type="float" value="" size="3" optional="True" |
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128 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/> |
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129 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200" |
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130 label="The x-axis label" help="" /> |
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131 <param argument="--yAxisLabel" type="text" value="genes" size="30" |
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132 label="The y-axis label for the top panel" help="" /> |
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133 |
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134 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100" |
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135 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/> |
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136 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100" |
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137 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/> |
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138 |
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139 <param argument="--whatToShow" type="select" label="What to show" |
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140 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> |
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141 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> |
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142 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option> |
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143 <option value="heatmap and colorbar">heatmap and colorbar</option> |
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144 </param> |
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145 |
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146 <param argument="--startLabel" type="text" value="TSS" size="10" |
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147 label="Label for the region start" |
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148 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. "peak start"." /> |
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149 <param argument="--endLabel" type="text" value="TES" size="10" |
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150 label="Label for the region end" |
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151 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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152 |
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153 <param argument="--referencePointLabel" type="text" value="TSS" size="10" |
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154 label="Reference point label" |
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155 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. "peak start" etc." /> |
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156 <param argument="--regionsLabel" type="text" value="genes" size="30" |
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157 label="Labels for the regions plotted in the heatmap" |
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158 help="If more than one region is being plotted then a list of labels separated by comma is required. For example, label1, label2."> |
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159 <sanitizer> |
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160 <valid initial="string.printable"> |
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161 </valid> |
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162 </sanitizer> |
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163 </param> |
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164 <expand macro="plotTitle" /> |
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165 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" |
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166 label="Do one plot per group" |
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167 help="When clustering is applied to the data, or the computematrix was performed on multiple BED files, |
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168 plot the groups next to each other. The default is to plot |
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169 the samples next to each other. If this option is set, each group (or cluster) will get its own plot, |
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170 with different samples stacked on top of each other."/> |
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171 |
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172 <expand macro="kmeans_clustering" /> |
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173 </when> |
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174 </conditional> |
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175 </inputs> |
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176 <outputs> |
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177 <expand macro="output_image_file_format" /> |
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178 <expand macro="output_graphic_outputs" /> |
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179 <expand macro="output_save_matrix_values" /> |
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180 </outputs> |
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181 <tests> |
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182 <test> |
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183 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> |
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184 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" /> |
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185 </test> |
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186 <test> |
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187 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> |
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188 <param name="showAdvancedOpt" value="yes" /> |
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189 <param name="whatToShow" value="heatmap and colorbar" /> |
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190 <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" /> |
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191 </test> |
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192 </tests> |
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193 <help> |
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194 <![CDATA[ |
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195 **What it does** |
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196 |
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197 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. |
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198 Like profiler, it requires that computeMatrix was run first to calculate the values. |
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199 |
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200 We have implemented number of optional parameters to optimize the visual output and we encourage you to play around with the min/max values |
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201 displayed in the heatmap as well as with the different coloring options. The most powerful option is the k-means/hierarchical clustering, |
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202 where you simply need to indicate the number of groups with similar read distributions that you expect and the algorithm will do the sorting for you. |
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203 |
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204 |
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205 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png |
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206 :alt: Heatmap of RNA Polymerase II ChIP-seq |
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207 |
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208 |
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209 You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotHeatmap.html |
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210 |
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211 |
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212 ----- |
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213 |
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214 @REFERENCES@ |
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215 ]]> |
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216 </help> |
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217 <expand macro="citations" /> |
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218 </tool> |