Mercurial > repos > bgruening > hicexplorer_hicplottads

annotate hicPlotTADs.xml @ 8:7e535e3b71f3 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:38:47 -0400
parents 94fff1a6a899
children
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5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>plot Hi-C contact matrices heatmaps alongside other data tracks</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotTADs</token>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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5 <import>macros.xml</import>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10
0
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11 sed '/^$/d' '$tracks_config' &&
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 @BINARY@
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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13 --tracks '$tracks_config'
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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14 #if $region and $region is not None:
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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15 --region '$region'
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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16 #end if
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17 --outFileName plot.$image_file_format
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18 && mv plot.$image_file_format plot
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19 ]]>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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20 </command>
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21 <configfiles>
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22 <configfile name="tracks_config">
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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23 #if $x_axis.x_axis_select == "yes":
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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24 [x-axis]
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25 #if $x_axis.fontsize:
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26 fontsize = $x_axis.fontsize
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27 #end if
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28 #if $x_axis.where:
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5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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29 where = $x_axis.where
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30 #end if
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31 #end if
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32 #for $counter, $track in enumerate($tracks):
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33 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
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34 [hic_section_$counter]
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35 file = $track.track_file_style_conditional.matrix_h5_cooler
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36 file_type = hic_matrix
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37 title = $track.track_file_style_conditional.title
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38 #if $track.track_file_style_conditional.depth:
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39 depth = $track.track_file_style_conditional.depth
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40 #end if
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41 #if $track.track_file_style_conditional.colormap:
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42 colormap = $track.track_file_style_conditional.colormap
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43 #end if
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44 #if $track.track_file_style_conditional.min_value:
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45 min_value = $track.track_file_style_conditional.min_value
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46 #end if
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47 #if $track.track_file_style_conditional.max_value:
2
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48 max_value = $track.track_file_style_conditional.max_value
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49 #end if
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50 transform = $track.track_file_style_conditional.transform
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51 width = $track.track_file_style_conditional.width_matrix
2
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52 #if $track.track_file_style_conditional.boundaries_file:
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53 boundaries_file = $track.track_file_style_conditional.boundaries_file
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54 #end if
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55 #if $track.track_file_style_conditional.x_labels:
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56 x labels = $track.track_file_style_conditional.x_labels
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57 #end if
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58 #if $track.track_file_style_conditional.type:
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59 type = $track.track_file_style_conditional.type
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60 #end if
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61 #if $track.track_file_style_conditional.show_masked_bins:
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62 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
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63 #end if
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64 #if $track.track_file_style_conditional.scale_factor:
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65 scale factor = $track.track_file_style_conditional.scale_factor
0
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66 #end if
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67
8
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68 #end if
2
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69 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
0
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70
2
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71 [tad_score_$counter]
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72 file = $track.track_file_style_conditional.track_input_bedgraph
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73 title = $track.track_file_style_conditional.title
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74 #if $track.track_file_style_conditional.color:
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75 color = $track.track_file_style_conditional.color
0
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76 #end if
2
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77 #if $track.track_file_style_conditional.width_tad:
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78 width = $track.track_file_style_conditional.width_tad
1
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79 #end if
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80 #if $track.track_file_style_conditional.type_lines:
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81 type = $track.track_file_style_conditional.type_lines
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82 #end if
2
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83 #if $track.track_file_style_conditional.show_data:
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84 show data range = $track.track_file_style_conditional.show_data
0
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85 #end if
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86
2
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87 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
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88 #if $columns > 5:
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89 file_type = bedgraph_matrix
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90 #else:
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91 file_type = bedgraph
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92 #end if
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93 type = lines
8
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94 #end if
2
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95 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
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96
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97 [chrom states_$counter]
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98 file = $track.track_file_style_conditional.track_input_bed
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99 title = $track.track_file_style_conditional.title
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100 #if $track.track_file_style_conditional.color:
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101 color = $track.track_file_style_conditional.color
0
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102 #end if
2
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103 display = collapsed
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104 #if $track.track_file_style_conditional.width_chrom:
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105 width = $track.track_file_style_conditional.width_chrom
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106 #end if
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107 #if $track.track_file_style_conditional.border_color:
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108 border_color = $track.track_file_style_conditional.border_color
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109 #end if
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110 file_type = bed
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111 #end if
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112 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
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113
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114 [genes_$counter]
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115 file = $track.track_file_style_conditional.track_input_bed
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116 title = $track.track_file_style_conditional.title
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117 #if $track.track_file_style_conditional.color:
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118 color = $track.track_file_style_conditional.color
8
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119 #end if
2
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120
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121 #if $track.track_file_style_conditional.width_bed:
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122 width = $track.track_file_style_conditional.width_bed
8
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123 #end if
0
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124
2
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125 #if $track.track_file_style_conditional.labels:
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126 labels = $track.track_file_style_conditional.labels
8
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127 #end if
2
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128
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129 #if $track.track_file_style_conditional.type:
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130 type = $track.track_file_style_conditional.type
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131 #end if
2
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132
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133 file_type = bed
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134 #if $track.track_file_style_conditional.fontsize:
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135 fontsize = $track.track_file_style_conditional.fontsize
8
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136 #end if
2
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137
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138 #if $track.track_file_style_conditional.gene_rows:
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139 gene rows = $track.track_file_style_conditional.gene_rows
8
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140 #end if
0
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141
2
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142 #if $track.track_file_style_conditional.global_max_row:
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143 global max row = $track.track_file_style_conditional.global_max_row
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144 #end if
2
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145
8
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146 #end if
2
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147
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148
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149 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
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150
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151 [bedgraph_$counter]
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152 file = $track.track_file_style_conditional.track_input_bedgraph
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153 title = $track.track_file_style_conditional.title
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154 #if $track.track_file_style_conditional.color:
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155 color = $track.track_file_style_conditional.color
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156 #end if
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157 #if $track.track_file_style_conditional.width_bedgraph:
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158 width = $track.track_file_style_conditional.width_bedgraph
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159 #end if
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160 #if $track.track_file_style_conditional.show_data:
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161 show data range = $track.track_file_style_conditional.show_data
0
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162 #end if
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163
2
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164 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
0
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165 #if $columns > 5:
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166 file_type = bedgraph_matrix
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167 #else:
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168 file_type = bedgraph
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169 #end if
2
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170 type = lines
8
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171 #end if
0
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172
2
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173 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
0
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174
2
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175 [bigwig_$counter]
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176 file = $track.track_file_style_conditional.track_input_bigwig
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177 title = $track.track_file_style_conditional.title
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178 color = $track.track_file_style_conditional.color
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179 #if $track.track_file_style_conditional.min_value:
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180 min_value = $track.track_file_style_conditional.min_value
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181 #else:
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182 min_value = 0
0
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183 #end if
2
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184 #if $track.track_file_style_conditional.max_value:
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185 max_value = $track.track_file_style_conditional.max_value
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186 #else:
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187 max_value = auto
0
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188 #end if
2
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189 width = $track.track_file_style_conditional.width_bigwig
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190 #if $track.track_file_style_conditional.number_of_bins:
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191 number of bins = $track.track_file_style_conditional.number_of_bins
0
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192 #end if
2
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193 nans to zeros = $track.track_file_style_conditional.nans_to_zeros
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194 #if $track.track_file_style_conditional.type_conditional == 'fill_option':
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195 type = fill
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196 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
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197 type = line:$track.track_file_style_conditional.type_conditional.width_line
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198 #elif $track.track_file_style_conditional.type_conditional == 'point_option':
2
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199 type = points:$track.track_file_style_conditional.type_conditional.width_point
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200 #end if
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201 #if $track.track_file_style_conditional.data_range:
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202 show data range = $track.track_file_style_conditional.data_range
0
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203 #end if
2
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204 file_type = bigwig
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205 #end if
2
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206 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
0
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207
2
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208 [bedgraph_matrix_$counter]
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209 file = $track.track_file_style_conditional.track_input_bedgraph_matrix
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210 title = $track.track_file_style_conditional.title
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211 #if $track.track_file_style_conditional.width_bedgraph:
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212 width = $track.track_file_style_conditional.width_bedgraph
0
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213 #end if
2
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214 orientation = inverted
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215 #if $track.track_file_style_conditional.min_value:
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216 min_value = $track.track_file_style_conditional.min_value
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217 #end if
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218 #if $track.track_file_style_conditional.max_value:
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219 max_value = $track.track_file_style_conditional.max_value
0
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220 #end if
2
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221 #if $track.track_file_style_conditional.type_lines:
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222 type = $track.track_file_style_conditional.type_lines
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223 #end if
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224 file_type = bedgraph_matrix
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225 plot horizontal lines=False
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226 #end if
2
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227 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
0
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228
2
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229 [vlines_$counter]
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230 file = $track.track_file_style_conditional.track_input_bed
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231 type = vlines
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232 file_type = bed
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233 #end if
2
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234 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
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235
0
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236 [spacer]
2
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237 #if $track.track_file_style_conditional.spacer_width:
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238 width = $track.track_file_style_conditional.spacer_width
0
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239 #end if
8
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240 #end if
0
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241 #end for</configfile>
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242 </configfiles>
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243 <inputs>
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244 <expand macro="region" />
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245
0
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246 <repeat name="tracks" min="1" title="Include tracks in your plot"
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247 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
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248 <conditional name="track_file_style_conditional">
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249 <param name="track_file_style_selector" type="select" label="Choose style of the track">
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250 <option value="hic_matrix_option">TAD visualization</option>
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251 <option value="chrom_states_option">Chromatine states</option>
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252 <option value="tad_score_track_option">TAD score</option>
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253 <option value="gene_track_option">Gene track / Bed track</option>
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254 <option value="bigwig_track_option">Bigwig track</option>
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255 <option value="bedgraph_track_option">Bedgraph track </option>
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256 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
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257 <option value="vlines_track_option">Vlines track</option>
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258 <option value="spacer_option">Spacer</option>
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259 </param>
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260 <when value="hic_matrix_option">
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261 <expand macro="plot_title" />
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262 <expand macro="matrix_h5_cooler_macro" />
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263
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264 <expand macro="colormap" />
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265 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
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266 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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267 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
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268 <param name="transform" type="select" label="Plot the transformed value">
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269 <option value="log1p" selected="True" >log1p</option>
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270 <option value="log">log</option>
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271 <option value="-log">-log</option>
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272
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273 </param>
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274 <param name="width_matrix" type="float" value="1.5" optional="True" label="Width"/>
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275
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276 <param name="type" type="select" optional="True" label="Plotting type">
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277 <option value="arcplot">arcplot</option>
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278 <option value="interaction">interaction</option>
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279 </param>
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280 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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281 label="Show masked bins" />
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282 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file"/>
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283 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
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284 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" />
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285
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286 </when>
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287 <when value="tad_score_track_option">
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288 <expand macro="plot_title" />
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289 <expand macro="track_input_bedgraph_macro" />
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290 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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291 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
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292 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
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293 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
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294 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
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295 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
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296 </when>
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297 <when value="chrom_states_option">
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298 <expand macro="plot_title" />
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299
2
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300 <expand macro="track_input_bed_macro" />
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301 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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302
2
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303 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
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304 <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/>
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305 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
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306 label="Plot labels" />
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307 </when>
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308 <when value="gene_track_option">
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309 <expand macro="plot_title" />
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310
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311 <expand macro="track_input_bed_macro" />
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312 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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313 <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/>
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314 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
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315 label="Plot labels" />
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316 <param name="type" type="select" optional="True" label="Type">
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317 <option value="genes">genes</option>
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318 <option value="domains">domains</option>
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319 </param>
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320 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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321 label="Global max rows" />
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322 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
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323 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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324
2
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325 </when>
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326 <when value="bedgraph_track_option">
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327 <expand macro="plot_title" />
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328 <expand macro="track_input_bedgraph_macro" />
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329 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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330
2
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331 <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/>
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332 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
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333 </when>
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334 <when value="bigwig_track_option">
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335 <expand macro="plot_title" />
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336
2
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337 <expand macro="track_input_bigwig_macro" />
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338 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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339
2
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340 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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341 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
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342
2
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343 <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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344 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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345 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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346 label="NAN's to zeros" />
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347 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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348 <param name="type_selector" type="select" label="Choose style of the plot.">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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349 <option value="fill_option">fill</option>
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350 <option value="line_option">line</option>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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351 <option value="point_option">point</option>
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352 </param>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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353 <when value="line_option">
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354 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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355 </when>
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356 <when value="point_option">
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357 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
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358 </when>
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359 <when value="fill_option" />
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360 </conditional>
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361 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
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362 </when>
8
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363
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364
2
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365 <when value="bedgraph_matrix_track_option">
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366 <expand macro="plot_title" />
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367
2
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368 <expand macro="track_input_bedgraph_matrix_macro" />
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369 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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370 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
0
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371
2
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372 <param name="width_bedgraph" type="float" value="1.5" optional="True" label="Width"/>
0
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373
2
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374 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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375 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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376 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
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377 </when>
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378 <when value="vlines_track_option">
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379 <expand macro="track_input_bed_macro" />
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380 </when>
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381 <when value="spacer_option">
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382 <expand macro="spacer_macro" />
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383 </when>
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384 </conditional>
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385
0
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386 </repeat>
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387
8
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388
0
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389 <conditional name="x_axis">
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390 <param name="x_axis_select" type="select" label="Configure x-axis">
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391 <option value="no" selected="True">No</option>
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392 <option value="yes">Yes</option>
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393 </param>
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394 <when value="yes">
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395 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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396 <param name="where" type="select" optional="True" label="Where to place the x-axis">
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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397 <option value="top">Top</option>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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398 <option value="bottom">Bottom</option>
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399 </param>
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400 </when>
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401 <when value="no" />
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402 </conditional>
2
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403 <param name="image_file_format" type="select" label="Image output format">
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404 <option value="png">png</option>
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405 <option value="svg">svg</option>
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406 </param>
0
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407 </inputs>
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408 <outputs>
8
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409 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
2
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410 <change_format>
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411 <when input="image_file_format" value="png" format="png" />
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412 <when input="image_file_format" value="svg" format="svg" />
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413 </change_format>
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414 </data>
0
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415 </outputs>
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416 <tests>
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417 <test>
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418 <param name="region" value="chrX:3000000-3500000"/>
2
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419 <conditional name="x_axis">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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420 <param name="x_axis_select" value="yes" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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421 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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422 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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423 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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424 <param name="track_file_style_selector" value="hic_matrix_option" />
5
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425 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
144bf28956a7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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426
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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427 <param name="title" value="Kc DpnII (Li et al. 2015)" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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428 <param name="colormap" value="RdYlBu_r" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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429 <param name="depth" value="200000" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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430 <param name="transform" value="log1p" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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431 <param name="boundaries_file" value="domains.bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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432 <param name="x_labels" value="True" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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433 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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434 </repeat>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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435 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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436 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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437 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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438 <param name="spacer_width" value="0.05" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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439 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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440 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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441 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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442 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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443 <param name="track_file_style_selector" value="chrom_states_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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444 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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445 <param name="title" value="TAD state" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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446 <param name="width_chrom" value="0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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447 <param name="labels" value="off" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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448 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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449 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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450 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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451 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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452 <param name="track_file_style_selector" value="tad_score_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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453 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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454 <param name="title" value="TAD separation score (Ramirez et al.)" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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455 <param name="width_tad" value="10" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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456 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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457 </repeat>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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458 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
459 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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460 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
461 <param name="spacer_width" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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462 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
463 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
464 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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465 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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466 <param name="track_file_style_selector" value="bedgraph_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
467 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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468 <param name="title" value="bedgraph" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
469 <param name="width_bedgraph" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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470 <param name="color" value="blue" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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471 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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472 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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473 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
474 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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475 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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476 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
477 <param name="title" value="rep 1 test fill" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
478 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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479 <param name="color" value="blue" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
480 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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481 <param name="type_selector" value="fill_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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482 </conditional>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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483 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
484 </repeat>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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485
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
486 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
487 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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488 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
489 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
490 <param name="title" value="rep 1 test line" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
491 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
492 <param name="color" value="red" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
493 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
494 <param name="type_selector" value="line_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
495 <param name="width_line" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
496 </conditional>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
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497 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
498 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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499
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
500 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
501 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
502 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
503 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
504 <param name="title" value="rep 1 test lw=0.2" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
505 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
506 <param name="color" value="red" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
507 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
508 <param name="type_selector" value="line_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
509 <param name="width_line" value="0.1" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
510
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
511 </conditional>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
512 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
513 </repeat>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
514
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
515 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
516 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
517 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
518 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
519 <param name="title" value="rep 1 test point:0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
520 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
521 <param name="color" value="black" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
522 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
523 <param name="type_selector" value="point_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
524 <param name="width_point" value="0.5" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
525
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
526 </conditional>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
527 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
528 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
529
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
530 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
531 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
532 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
533 <param name="spacer_width" value="0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
534 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
535 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
536 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
537 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
538 <param name="track_file_style_selector" value="gene_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
539 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
540 <param name="title" value="genes" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
541 <param name="width_bed" value="5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
542 <param name="fontsize" value="10" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
543 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
544 </repeat>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
545 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
546 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
547 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
548 <param name="spacer_width" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
549 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
550 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
551 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
552 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
553 <param name="track_file_style_selector" value="gene_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
554 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
555 <param name="title" value="max num rows 3" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
556 <param name="width_bed" value="3" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
557 <param name="fontsize" value="8" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
558 <param name="gene_rows" value="3" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
559 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
560 </repeat>
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
561 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
562 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
563 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
564 <param name="spacer_width" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
565 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
566 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
567 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
568 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
569 <param name="track_file_style_selector" value="gene_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
570 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
571 <param name="title" value="bed6 global max row" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
572 <param name="width_bed" value="20" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
573 <param name="fontsize" value="10" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
574 <param name="global_max_row" value="True" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
575 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
576 </repeat>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
577 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
578 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
579 <param name="track_file_style_selector" value="vlines_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
580 <param name="track_input_bed" value="domains.bed" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
581 <param name="type" value="vlines" />
8
7e535e3b71f3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
582 </conditional>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
583 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
584 <param name="image_file_format" value="png" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
585 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
586 </test>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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587 </tests>
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588 <help><![CDATA[
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589
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590 Plot Topologic Associated Domains
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591 =================================
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592
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593 **hicPlotTADs** is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene, ChIP-seq, RNA-seq or other tracks, including TAD seperation scores computed by ``hicFindTADs``.
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594
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595 _________________
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596
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597 Usage
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598 -----
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599
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600 This tool takes various types of tracks as input:
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601
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602 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
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603 - **Chromatin states:** display blocks of different colors following a bed file.
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604 - **TAD score:** display TAD seperation score computed by ``hicFindTADs``.
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605 - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.
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606 - **Bigwig track:** generic bigwig track plotting.
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607 - **Bedgraph track:** generic bedgraph track plotting.
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608 - **Bedgraph matrix track** is used to specifically plot bm files computed by ``hicFindTADs`` (TAD seperation scores).
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609 - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by ``hicFindTADs``.
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610 - **Spacer:** Add some space between two tracks.
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611
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612 For each track, parameters for the color, the width or the font size can be defined.
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613
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614 _________________
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615
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616 Output
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617 ------
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618
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619 **hicPlotTADs** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) also contains Hi-C data. The plot is composed of tracks that need to be specified.
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620 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **hicPlotTADs**. TADs were computed by ``hicFindTADs``. The additional tracks added correspond to: TAD-separation score (as reported by ``hicFindTADs``), chromatin states, principal component 1 (A/B compartment) computed using ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
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621
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622 .. image:: $PATH_TO_IMAGES/hicPlotTADs.png
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623 :width: 70 %
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624
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625 _________________
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626
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627 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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628
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629 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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630 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
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631 ]]></help>
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632 <expand macro="citations" />
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633 </tool>