Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate hicPlotMatrix.xml @ 3:00855c36a2cb draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 1beb50fdb3f5f8fd60e3b9c3d44964d70075616d
author iuc
date Mon, 27 Nov 2017 11:16:12 -0500
parents 2c0069f645bc
children fd5e51d2b558
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 detect_errors="exit_code"><![CDATA[
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9 ln -s '$matrix' input_matrix.h5 &&
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11 @BINARY@
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13 --matrix input_matrix.h5
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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15 #if $title and $title is not None:
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16 --title '$title'
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17 #end if
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19 #if $scoreName and $scoreName is not None:
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20 --scoreName '$scoreName'
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21 #end if
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24 --outFileName plot.$image_file_format
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26 $perChromosome
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27 $clearMaskedBins
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28
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29 --whatToShow '$whatToShow.whatToShow_select'
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32 ## special: --chromosomeOrder is optional, but if given needs at least one argument
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33 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
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34 #if chroms:
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35 --chromosomeOrder '$chroms'
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36 #end if
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37
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38 #if $region:
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39 --region '$region'
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40 #end if
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a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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42 #if $region2:
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43 --region2 '$region2'
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44 #end if
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45 $log1p
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46 $log
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47
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48 #if $colormap:
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49 --colorMap $colormap
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50 #end if
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52 #if $vMin:
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53 --vMin $vMin
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54 #end if
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55
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56 #if $vMax:
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57 --vMax $vMax
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58 #end if
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59
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60 #if $whatToShow.whatToShow_select != 'heatmap':
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61 #if $whatToShow.zMax:
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62 --zMax $whatToShow.zMax
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63 #end if
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64 #end if
2
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65 && mv plot.$image_file_format plot
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66 ]]>
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67 </command>
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68 <inputs>
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69 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/>
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70 <param argument="--title" type="text" optional="true" label="Plot title"/>
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71 <param argument="--scoreName" type="text" optional="true" label="Score name"/>
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72 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
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73 label="Plot per chromosome"
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74 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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75 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
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76 label="Remove masked bins from the matrix" />
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77
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78 <conditional name="whatToShow">
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79 <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D">
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80 <option value="both">Show both</option>
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81 <option value="heatmap" selected="true">Only heatmap</option>
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82 <option value="3D">Only 3D</option>
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83 </param>
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84 <when value="both">
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85 <expand macro="zMax" />
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86 </when>
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87 <when value="3D">
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88 <expand macro="zMax" />
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89 </when>
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90 <when value="heatmap"/>
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91 </conditional>
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92
2
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93 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
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94 help="This option overrides --region and --region2" >
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95 <param name="chromosome" type="text" >
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96 <validator type="empty_field" />
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97 </param>
0
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98 </repeat>
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99
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100 <param argument="--region" type="text" optional="True" label="Plot only this region"
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101 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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102 <param argument="--region2" type="text" optional="True" label="Region two to plot"
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103 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
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104 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
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105 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the *MINUS* log of the matrix values."/>
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106
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107 <expand macro="colormap" />
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108
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109 <param argument="--vMin" type="float" optional="true" label="vMin"/>
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110 <param argument="--vMax" type="float" optional="true" label="vMax"/>
2
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111 <param name="image_file_format" type="select" label="Image output format">
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112 <option value="png" selected="True">png</option>
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113 <option value="svg">svg</option>
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114 </param>
0
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115 </inputs>
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116 <outputs>
2
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117 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}">
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118 <change_format>
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119 <when input="image_file_format" value="svg" format="svg" />
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120 </change_format>
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121 </data>
0
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122 </outputs>
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123 <tests>
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124 <test>
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125 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/>
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126 <param name="region" value="chrX:3000000-3500000"/>
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127 <param name="region2" value="chrX:3100000-3600000"/>
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128 <param name="log1p" value="True"/>
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129 <param name="clearMaskedBins" value="True"/>
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130 <param name="whatToShow_select" value="heatmap"/>
2
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131 <param name="image_file_format" value="png" />
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132 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
0
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136
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137 **What it does**
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138
2
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139 Plots a Hi-C matrix heatmap.
0
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140
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141 ]]></help>
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142 <expand macro="citations" />
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143 </tool>
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144