Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate hicPlotMatrix.xml @ 0:70cdd1d37637 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
author bgruening
date Sun, 09 Oct 2016 17:35:10 -0400
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children 8116270ba934
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70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Plots a HiC matrix heatmap</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotMatrix</token>
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5 <import>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 ln -s '$matrix' input_matrix.npz.h5 &&
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12 @BINARY@
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13
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14 --matrix input_matrix.npz.h5
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16 #if $title and $title is not None:
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17 --title '$title'
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18 #end if
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20 #if $scoreName and $scoreName is not None:
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21 --scoreName '$scoreName'
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22 #end if
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23
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24 #if $outFileName and $outFileName is not None:
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25 --outFileName plot.png
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26 #end if
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28 $perChromosome
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29 $clearMaskedBins
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30
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32 --whatToShow $whatToShow.whatToShow_select
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35 ## special: --chromosomeOrder is optional, but if given needs at least one argument
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36 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
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37 #if chroms
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38 --chromosomeOrder "$chroms"
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39 #end if
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40
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41 #if $region and $region is not None:
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42 --region $region
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43 #end if
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44
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45 #if $region2 and $region2 is not None:
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46 --region2 $region2
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47 #end if
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48 $log1p
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49 $log
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50
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51 #if $colorMap and $colorMap is not None:
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52 --colorMap $colorMap
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53 #end if
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54
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55 #if $vMin and $vMin is not None:
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56 --vMin $vMin
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57 #end if
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58
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59 #if $vMax and $vMax is not None:
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60 --vMax $vMax
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61 #end if
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62
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63 #if $whatToShow.whatToShow_select != 'heatmap':
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64 --zMax $zMax
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65 #end if
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66
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67 ]]>
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68 </command>
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69 <inputs>
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70 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/>
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71 <param argument="--title" type="text" optional="true" label="Plot title"/>
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72 <param argument="--scoreName" type="text" optional="true" label="Score name"/>
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73 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
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74 label="Plot per chromosome"
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75 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
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76 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
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77 label="Remove masked bins from the matrix" />
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78
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79 <conditional name="whatToShow">
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80 <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D">
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81 <option value="both" selected="true">Show both</option>
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82 <option value="heatmap">Only heatmap</option>
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83 <option value="3D">Only 3D</option>
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84 </param>
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85 <when value="both">
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86 <expand macro="zMax" />
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87 </when>
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88 <when value="3D">
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89 <expand macro="zMax" />
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90 </when>
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91 <when value="heatmap"/>
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92 </conditional>
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93
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94 <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):" help="This option overrides --region and --region2">
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95 <param name="chromosome" type="text" />
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96 </repeat>
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97
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98 <param argument="--region" type="text" label="Plot only this region"
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99 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
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100 <param argument="--region2" type="text" label="If given then only the region defined by --region and --region2 is given. The format is the same as --region1"/>
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101 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
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102 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the *MINUS* log of the matrix values."/>
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103
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104 <expand macro="colormap" />
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105
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106 <param argument="--vMin" type="float" optional="true" label="vMin"/>
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107 <param argument="--vMax" type="float" optional="true" label="vMax"/>
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108 <param argument="--zMax" type="float" optional="true" label="zMax" help="For 3D plots"/>
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109
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110 </inputs>
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111 <outputs>
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112 <data name="outFileName" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
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113 </outputs>
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114 <tests>
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115 <test>
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116 <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
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117 <param name="whatToShow_select" value="heatmap"/>
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118 <output name="outFileName" file="hicPlotMatrix_result1.png" ftype="png" compare="sim_size"/>
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119 </test>
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120 </tests>
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121 <help><![CDATA[
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122
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123 **What it does**
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124
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125 Plots a HiC matrix heatmap.
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126
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127 ]]></help>
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128 <expand macro="citations" />
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129 </tool>
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130