Mercurial > repos > bgruening > hicexplorer_hicplottads

annotate hicPlotTADs.xml @ 6:36ef3cb8ae2e draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
author iuc
date Tue, 02 Jan 2018 10:20:13 -0500
parents 144bf28956a7
children 94fff1a6a899
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1 <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotTADs</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
5
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10
0
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11 sed '/^$/d' '$tracks_config' &&
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12 @BINARY@
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13 --tracks '$tracks_config'
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14 #if $region and $region is not None:
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15 --region '$region'
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16 #end if
2
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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 ]]>
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20 </command>
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21 <configfiles>
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22 <configfile name="tracks_config">
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23 #if $x_axis.x_axis_select == "yes":
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24 [x-axis]
1
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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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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
2
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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:
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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 #if $track.track_file_style_conditional.boundaries_file:
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52 boundaries_file = $track.track_file_style_conditional.boundaries_file
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53 #end if
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54 #if $track.track_file_style_conditional.x_labels:
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55 x labels = $track.track_file_style_conditional.x_labels
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56 #end if
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57 #if $track.track_file_style_conditional.type:
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58 type = $track.track_file_style_conditional.type
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59 #end if
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60 #if $track.track_file_style_conditional.show_masked_bins:
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61 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
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62 #end if
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63 #if $track.track_file_style_conditional.scale_factor:
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64 scale factor = $track.track_file_style_conditional.scale_factor
0
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65 #end if
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66
2
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67 #end if
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68 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
0
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69
2
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70 [tad_score_$counter]
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71 file = $track.track_file_style_conditional.track_input_bedgraph
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72 title = $track.track_file_style_conditional.title
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73 #if $track.track_file_style_conditional.color:
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74 color = $track.track_file_style_conditional.color
0
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75 #end if
2
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76 #if $track.track_file_style_conditional.width_tad:
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77 width = $track.track_file_style_conditional.width_tad
1
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78 #end if
2
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79 #if $track.track_file_style_conditional.show_data:
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80 show data range = $track.track_file_style_conditional.show_data
0
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81 #end if
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82
2
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83 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
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84 #if $columns > 5:
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85 file_type = bedgraph_matrix
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86 #else:
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87 file_type = bedgraph
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88 #end if
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89 type = lines
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90 #end if
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91 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
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92
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93 [chrom states_$counter]
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94 file = $track.track_file_style_conditional.track_input_bed
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95 title = $track.track_file_style_conditional.title
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96 #if $track.track_file_style_conditional.color:
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97 color = $track.track_file_style_conditional.color
0
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98 #end if
2
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99 display = collapsed
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100 #if $track.track_file_style_conditional.width_chrom:
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101 width = $track.track_file_style_conditional.width_chrom
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102 #end if
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103 #if $track.track_file_style_conditional.border_color:
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104 border_color = $track.track_file_style_conditional.border_color
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105 #end if
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106 file_type = bed
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107 #end if
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108 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
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109
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110 [genes_$counter]
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111 file = $track.track_file_style_conditional.track_input_bed
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112 title = $track.track_file_style_conditional.title
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113 #if $track.track_file_style_conditional.color:
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114 color = $track.track_file_style_conditional.color
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115 #end if
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116
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117 #if $track.track_file_style_conditional.width_bed:
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118 width = $track.track_file_style_conditional.width_bed
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119 #end if
0
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120
2
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121 #if $track.track_file_style_conditional.labels:
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122 labels = $track.track_file_style_conditional.labels
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123 #end if
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124
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125 #if $track.track_file_style_conditional.type:
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126 type = $track.track_file_style_conditional.type
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127 #end if
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128
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129 file_type = bed
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130 #if $track.track_file_style_conditional.fontsize:
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131 fontsize = $track.track_file_style_conditional.fontsize
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132 #end if
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133
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134 #if $track.track_file_style_conditional.gene_rows:
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135 gene rows = $track.track_file_style_conditional.gene_rows
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136 #end if
0
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137
2
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138 #if $track.track_file_style_conditional.global_max_row:
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139 global max row = $track.track_file_style_conditional.global_max_row
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140 #end if
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141
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142 #end if
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143
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144
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145 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
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146
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147 [bedgraph_$counter]
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148 file = $track.track_file_style_conditional.track_input_bedgraph
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149 title = $track.track_file_style_conditional.title
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150 #if $track.track_file_style_conditional.color:
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151 color = $track.track_file_style_conditional.color
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152 #end if
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153 #if $track.track_file_style_conditional.width_bedgraph:
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154 width = $track.track_file_style_conditional.width_bedgraph
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155 #end if
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156 #if $track.track_file_style_conditional.show_data:
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157 show data range = $track.track_file_style_conditional.show_data
0
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158 #end if
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159
2
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160 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
0
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161 #if $columns > 5:
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162 file_type = bedgraph_matrix
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163 #else:
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164 file_type = bedgraph
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165 #end if
2
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166 type = lines
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167 #end if
0
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168
2
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169 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
0
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170
2
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171 [bigwig_$counter]
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172 file = $track.track_file_style_conditional.track_input_bigwig
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173 title = $track.track_file_style_conditional.title
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174 color = $track.track_file_style_conditional.color
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175 #if $track.track_file_style_conditional.min_value:
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176 min_value = $track.track_file_style_conditional.min_value
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177 #else:
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178 min_value = 0
0
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179 #end if
2
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180 #if $track.track_file_style_conditional.max_value:
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181 max_value = $track.track_file_style_conditional.max_value
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182 #else:
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183 max_value = auto
0
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184 #end if
2
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185 width = $track.track_file_style_conditional.width_bigwig
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186 #if $track.track_file_style_conditional.number_of_bins:
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187 number of bins = $track.track_file_style_conditional.number_of_bins
0
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188 #end if
2
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189 nans to zeros = $track.track_file_style_conditional.nans_to_zeros
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190 #if $track.track_file_style_conditional.type_conditional == 'fill_option':
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191 type = fill
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192 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
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193 type = line:$track.track_file_style_conditional.type_conditional.width_line
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194 #elif $track.track_file_style_conditional.type_conditional == 'point_option':
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195 type = points:$track.track_file_style_conditional.type_conditional.width_point
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196 #end if
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197 #if $track.track_file_style_conditional.data_range:
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198 show data range = $track.track_file_style_conditional.data_range
0
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199 #end if
2
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200 file_type = bigwig
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201 #end if
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202 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
0
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203
2
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204 [bedgraph_matrix_$counter]
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205 file = $track.track_file_style_conditional.track_input_bedgraph_matrix
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206 title = $track.track_file_style_conditional.title
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207 #if $track.track_file_style_conditional.width_bedgraph:
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208 width = $track.track_file_style_conditional.width_bedgraph
0
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209 #end if
2
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210 orientation = inverted
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211 #if $track.track_file_style_conditional.min_value:
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212 min_value = $track.track_file_style_conditional.min_value
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213 #end if
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214 #if $track.track_file_style_conditional.max_value:
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215 max_value = $track.track_file_style_conditional.max_value
0
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216 #end if
2
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217 #if $track.track_file_style_conditional.type_lines:
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218 type = $track.track_file_style_conditional.type_lines
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219 #end if
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220 file_type = bedgraph_matrix
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221 plot horizontal lines=False
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222 #end if
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223 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
0
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224
2
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225 [vlines_$counter]
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226 file = $track.track_file_style_conditional.track_input_bed
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227 type = vlines
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228 file_type = bed
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229 #end if
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230 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
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231
0
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232 [spacer]
2
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233 #if $track.track_file_style_conditional.spacer_width:
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234 width = $track.track_file_style_conditional.spacer_width
0
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235 #end if
2
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236 #end if
0
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237 #end for</configfile>
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238 </configfiles>
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239 <inputs>
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240 <expand macro="region" />
2
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241
0
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242 <repeat name="tracks" min="1" title="Include tracks in your plot"
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243 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
2
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244 <conditional name="track_file_style_conditional">
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245 <param name="track_file_style_selector" type="select" label="Choose style of the track">
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246 <option value="hic_matrix_option">TAD visualization</option>
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247 <option value="chrom_states_option">Chromatine states</option>
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248 <option value="tad_score_track_option">TAD score</option>
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249 <option value="gene_track_option">Gene track</option>
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250 <option value="bigwig_track_option">Bigwig track</option>
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251 <option value="bedgraph_track_option">Bedgraph track </option>
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252 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
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253 <option value="vlines_track_option">Vlines track</option>
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254 <option value="spacer_option">Spacer</option>
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255 </param>
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256 <when value="hic_matrix_option">
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257 <expand macro="plot_title" />
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258 <expand macro="matrix_h5_cooler_macro" />
2
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259
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260 <expand macro="colormap" />
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261 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
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262 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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263 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
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264 <param name="transform" type="select" label="Plot the transformed value">
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265 <option value="log1p" selected="True" >log1p</option>
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266 <option value="log">log</option>
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267 <option value="-log">-log</option>
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268
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269 </param>
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270 <param name="type" type="select" optional="True" label="Plotting type">
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271 <option value="arcplot">arcplot</option>
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272 <option value="interaction">interaction</option>
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273 </param>
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274 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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275 label="Show masked bins" />
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276 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file"/>
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277 <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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278 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" />
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279
2
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280 </when>
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281 <when value="tad_score_track_option">
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282 <expand macro="plot_title" />
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283 <expand macro="track_input_bedgraph_macro" />
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284 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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285
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286 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
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287 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
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288 </when>
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289 <when value="chrom_states_option">
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290 <expand macro="plot_title" />
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291
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292 <expand macro="track_input_bed_macro" />
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293 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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294
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295 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
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296 <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/>
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297 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
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298 label="Plot labels" />
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299 </when>
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300 <when value="gene_track_option">
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301 <expand macro="plot_title" />
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302
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303 <expand macro="track_input_bed_macro" />
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304 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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305 <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/>
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306 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
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307 label="Plot labels" />
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308 <param name="type" type="select" optional="True" label="Type">
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309 <option value="genes">genes</option>
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310 <option value="domains">domains</option>
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311 </param>
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312 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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313 label="Global max rows" />
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314 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
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315 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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316
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317 </when>
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318 <when value="bedgraph_track_option">
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319 <expand macro="plot_title" />
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320 <expand macro="track_input_bedgraph_macro" />
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321 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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322
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323 <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/>
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324 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
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325 </when>
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326 <when value="bigwig_track_option">
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327 <expand macro="plot_title" />
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328
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329 <expand macro="track_input_bigwig_macro" />
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330 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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331
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332 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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333 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
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334
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335 <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/>
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336 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
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337 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
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338 label="NAN's to zeros" />
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339 <conditional name="type_conditional">
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340 <param name="type_selector" type="select" label="Choose style of the plot.">
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341 <option value="fill_option">fill</option>
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342 <option value="line_option">line</option>
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343 <option value="point_option">point</option>
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344 </param>
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345 <when value="line_option">
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346 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
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347 </when>
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348 <when value="point_option">
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349 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
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350 </when>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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351 <when value="fill_option" />
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352 </conditional>
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353 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
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354 </when>
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355
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356
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357 <when value="bedgraph_matrix_track_option">
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358 <expand macro="plot_title" />
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359
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360 <expand macro="track_input_bedgraph_matrix_macro" />
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361 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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362 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
0
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363
2
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364 <param name="width_bedgraph" type="float" value="1.5" optional="True" label="Width"/>
0
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365
2
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366 <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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367 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
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368 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
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369 </when>
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370 <when value="vlines_track_option">
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371 <expand macro="track_input_bed_macro" />
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372 </when>
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373 <when value="spacer_option">
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374 <expand macro="spacer_macro" />
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375 </when>
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376 </conditional>
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377
0
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378 </repeat>
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379
2
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380
0
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381 <conditional name="x_axis">
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382 <param name="x_axis_select" type="select" label="Configure x-axis">
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383 <option value="no" selected="True">No</option>
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384 <option value="yes">Yes</option>
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385 </param>
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386 <when value="yes">
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387 <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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388 <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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389 <option value="top">Top</option>
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390 <option value="bottom">Bottom</option>
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391 </param>
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392 </when>
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393 <when value="no" />
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394 </conditional>
2
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395 <param name="image_file_format" type="select" label="Image output format">
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396 <option value="png">png</option>
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397 <option value="svg">svg</option>
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398 </param>
0
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399 </inputs>
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400 <outputs>
2
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401 <data format="png" name="outFileName" from_work_dir="plot">
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402 <change_format>
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403 <when input="image_file_format" value="png" format="png" />
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404 <when input="image_file_format" value="svg" format="svg" />
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405 </change_format>
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406 </data>
0
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407 </outputs>
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408 <tests>
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409 <test>
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410 <param name="region" value="chrX:3000000-3500000"/>
2
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411 <conditional name="x_axis">
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412 <param name="x_axis_select" value="yes" />
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413 </conditional>
0
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414 <repeat name="tracks">
2
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415 <conditional name="track_file_style_conditional">
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416 <param name="track_file_style_selector" value="hic_matrix_option" />
5
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417 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
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418
2
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419 <param name="title" value="Kc DpnII (Li et al. 2015)" />
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420 <param name="colormap" value="RdYlBu_r" />
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421 <param name="depth" value="200000" />
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422 <param name="transform" value="log1p" />
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423 <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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parents: 1
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424 <param name="x_labels" value="True" />
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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425 </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
426 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
427 <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
428 <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
429 <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
430 <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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parents: 1
diff changeset
431 </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
432 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
433 <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
434 <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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435 <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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parents: 1
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436 <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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parents: 1
diff changeset
437 <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
diff changeset
438 <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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parents: 1
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439 <param name="labels" value="off" />
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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440 </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
441 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
442 <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
443 <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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444 <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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parents: 1
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445 <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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446 <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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447 <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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448 </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
449 </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
450 <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
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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parents: 1
diff changeset
452 <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
453 <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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parents: 1
diff changeset
454 </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
455 </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
456 <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
457 <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
458 <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
459 <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
diff changeset
460 <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
461 <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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parents: 1
diff changeset
462 <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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parents: 1
diff changeset
463 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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464 </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
465 <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
466 <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
467 <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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parents: 1
diff changeset
468 <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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parents: 1
diff changeset
469 <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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parents: 1
diff changeset
470 <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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parents: 1
diff changeset
471 <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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parents: 1
diff changeset
472 <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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parents: 1
diff changeset
473 <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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parents: 1
diff changeset
474 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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475 </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
476 </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
477
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
478 <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
479 <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
480 <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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parents: 1
diff changeset
481 <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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parents: 1
diff changeset
482 <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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parents: 1
diff changeset
483 <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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parents: 1
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484 <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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parents: 1
diff changeset
485 <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
486 <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
487 <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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488 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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489 </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
490 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
491
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
492 <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
493 <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
494 <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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parents: 1
diff changeset
495 <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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parents: 1
diff changeset
496 <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
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parents: 1
diff changeset
497 <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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parents: 1
diff changeset
498 <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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parents: 1
diff changeset
499 <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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parents: 1
diff changeset
500 <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
501 <param name="width_line" value="0.1" />
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
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
503 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
504 </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
505 </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
506
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
507 <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
508 <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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diff changeset
509 <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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parents: 1
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510 <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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parents: 1
diff changeset
511 <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
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diff changeset
512 <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
513 <param name="color" value="black" />
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
514 <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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parents: 1
diff changeset
515 <param name="type_selector" value="point_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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516 <param name="width_point" value="0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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517
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
518 </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
519 </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
520 </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
521
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
522 <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
523 <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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524 <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
525 <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
526 </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
527 </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
528 <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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diff changeset
529 <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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diff changeset
530 <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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diff changeset
531 <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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532 <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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533 <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
534 <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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535 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
536 </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
537 <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
538 <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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539 <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
540 <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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541 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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542 </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
543 <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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544 <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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545 <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
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546 <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
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547 <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
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parents: 1
diff changeset
548 <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
549 <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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550 <param name="gene_rows" value="3" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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551 </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
552 </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
553 <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
554 <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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555 <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
556 <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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parents: 1
diff changeset
557 </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
558 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
559 <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
560 <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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561 <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
562 <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
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563 <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
564 <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
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565 <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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diff changeset
566 <param name="global_max_row" value="True" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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567 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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568 </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
569 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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570 <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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571 <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
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572 <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
573 <param name="type" value="vlines" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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574 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
575 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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576 <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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577 <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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578 </test>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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579 </tests>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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580 <help><![CDATA[
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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581
4
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
582 Plot TADs
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
583 =========
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
584
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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parents: 2
diff changeset
585 ``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 tracks.
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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586
4
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
587 Input
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
588 -----
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
589 - the region to plot: chr1:1000-2000
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
590 - the tracks:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
591 - the contact matrix
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
592 - Boundaries file: The result of ``hicFindTADs``.
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
593 - different tracks for comparison:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
594 - Chromatine states:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
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595 - TAD score
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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596 - gene tracks
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
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597 - Generic bigwig, bedgraph or bedgraph matrix files
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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598 - Vlines: vertical lines as a visual support where regions start / end over all tracks
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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599 - Spacer: Add some space between the different tracks
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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600
4
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
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601 For each track parameters for the color, the width or the font size can be defined.
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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parents: 2
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602
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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603 Output
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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604 ------
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
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605 An output looks like this:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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parents: 2
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606
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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parents: 2
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607
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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608 .. image:: $PATH_TO_IMAGES/master_TADs_plot.png
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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parents: 2
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609 :width: 80 %
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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610
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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611 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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612
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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613 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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614 ]]></help>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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615 <expand macro="citations" />
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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616 </tool>