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28
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1 <tool id="circos_graph" name="Circos" version="1.1.0">
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2
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3 <description>plots</description>
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4
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5 <command interpreter="perl">circos/bin/circos
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6
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7 -conf '$circos_config_file'
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8 -outputfile '${outputfile}.dat'
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9 -png
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10
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11 > '$log_file'
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12
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13 ;
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14
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15 rm '$outputfile'; ln -s '${outputfile}.png' '$outputfile'
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16
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17 </command>
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18
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19
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20 <inputs>
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21 <param name="graph_name" type="text" size="20" value="graph1" label="Graph name"/>
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22
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23 <param name="karyotype" type="select" format="txt" label="Type of model organism">
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24 <option value="data/karyotype.human_hg19.txt">Human (homo sapiens, hs) -hg19-</option>
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25 <option value="data/karyotype.human.txt">Human (homo sapiens, hs) -hg18-</option>
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26 <option value="data/2/karyotype.mouse.txt">Mouse (Mus Musculus, mm)</option>
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27 <option value="data/2/karyotype.dog.txt">Dog (Canis familiaris, cf)</option>
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28 <option value="data/2/karyotype.rt.txt">Rat (Rattus norvegicus, rn)</option>
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29 <option value="data/karyotype.yeast.txt">Yeast (Saccharomyces Cerevisiae, sc) -SGD-</option>
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30
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31 </param>
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32 <param name="chromosomes_units" type="integer" size="50" value="1000000" label="Chromosomes units"/>
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33 <param name="chromosomes" type="text" size="100" value="" label="List of chromosome names to keep or exclude" help="ex: hs2;hs3 or -hsX;-hsY">
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34 <sanitizer>
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35 <valid initial="string.printable">
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36 <add value=";"/>
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37 </valid>
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38 </sanitizer>
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39 </param>
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40 <param name="link_file" format="segdup" type="data" label="Input link file (.segdup)"/>
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41 </inputs>
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42
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43 <outputs>
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44 <data format="txt" name="log_file" label="${graph_name}.circos.log"/>
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45 <data format="png" name="outputfile" label="${graph_name}.png"/>
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46 </outputs>
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47
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48
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49
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50 <configfiles>
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51 <configfile name="ideogram_config_file">
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52
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53 <ideogram>
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54
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55 <spacing>
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56
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57 default = 5u
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58 break = 1u
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59
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60 axis_break_at_edge = yes
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61 axis_break = yes
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62 axis_break_style = 2
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63
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64 <break_style 1>
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65 stroke_color = black
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66 fill_color = blue
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67 thickness = 0.25r
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68 stroke_thickness = 2
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69 </break>
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70
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71 <break_style 2>
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72 stroke_color = black
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73 stroke_thickness = 3p
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74 thickness = 1.5r
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75 </break>
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76
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77 </spacing>
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78
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79 ## thickness (px) of chromosome ideogram
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80 thickness = 100p
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81 stroke_thickness = 2
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82 ## ideogram border color
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83 stroke_color = black
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84 fill = yes
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85 ## the default chromosome color is set here and any value
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86 ## defined in the karyotype file overrides it
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87 fill_color = black
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88
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89 ## fractional radius position of chromosome ideogram within image
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90 radius = 0.85r
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91 show_label = yes
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92 label_with_tag = yes
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93 label_font = condensedbold
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94 label_radius = dims(ideogram,radius) + 0.075r
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95 label_size = 60p
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96
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97 ## cytogenetic bands
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98 band_stroke_thickness = 2
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99
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100 ## show_bands determines whether the outline of cytogenetic bands
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101 ## will be seen
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102 show_bands = yes
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103 ## in order to fill the bands with the color defined in the karyotype
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104 ## file you must set fill_bands
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105 fill_bands = yes
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106
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107 </ideogram>
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108
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109 </configfile>
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110
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111 <configfile name="ticks_config_file">
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112
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113 show_ticks = yes
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114 show_tick_labels = yes
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115
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116 <ticks>
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117 radius = dims(ideogram,radius_outer)
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118 multiplier = 1e-6
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119
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120 <tick>
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121 spacing = 0.5u
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122 size = 2p
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123 thickness = 2p
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124 color = grey
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125 show_label = no
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126 label_size = 12p
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127 label_offset = 0p
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128 format = %.2f
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129 </tick>
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130
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131 <tick>
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132 spacing = 1u
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133 size = 3p
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134 thickness = 2p
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135 color = dgrey
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136 show_label = no
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137 label_size = 12p
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138 label_offset = 0p
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139 format = %.2f
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140 </tick>
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141
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142 <tick>
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143 spacing = 5u
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144 size = 5p
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145 thickness = 2p
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146 color = black
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147 show_label = yes
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148 label_size = 16p
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149 label_offset = 0p
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150 format = %d
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151 </tick>
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152
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153 <tick>
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154 spacing = 10u
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155 size = 8p
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156 thickness = 2p
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157 color = black
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158 show_label = yes
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159 label_size = 20p
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160 label_offset = 5p
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161 format = %d
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162 </tick>
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163 </ticks>
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164 </configfile>
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165
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166
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167 <configfile name="circos_config_file">
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168 <colors>
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169 <<include etc/colors.conf>>
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170 </colors>
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171
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172 <fonts>
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173 <<include etc/fonts.conf>>
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174 </fonts>
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175
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176 <<include $ideogram_config_file>>
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177 <<include $ticks_config_file>>
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178
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179 karyotype = $karyotype
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180
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181 <image>
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182 24bit = yes
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183 ##png = yes
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184 ##svg = no
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185 ## radius of inscribed circle in image
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186 radius = 1500p
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187 background = white
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188 ## by default angle=0 is at 3 o'clock position
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189 angle_offset = -90
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190 #angle_orientation = counterclockwise
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191
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192 auto_alpha_colors = yes
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193 auto_alpha_steps = 5
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194 </image>
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195
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196 chromosomes_units= $chromosomes_units
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197
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198 #if str($chromosomes)==""
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199 chromosomes_display_default = yes
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200 #else
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201 chromosomes_display_default = no
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202 chromosomes = $chromosomes
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203 #end if
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204
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205 <links>
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206
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207 z = 0
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208 radius = 0.95r
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209 bezier_radius = 0.2r
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210
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211 <link segdup>
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212 show = yes
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213 color = dgrey_a5
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214 thickness = 2
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215 file = $link_file
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216 record_limit = 1000
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217 </link>
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218
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219 </links>
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220
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221
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222 anglestep = 0.5
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223 minslicestep = 10
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224 beziersamples = 40
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225 debug = no
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226 warnings = no
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227 imagemap = no
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228
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229 units_ok = bupr
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230 units_nounit = n
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231 </configfile>
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232 </configfiles>
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233
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234 <help>
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235 **What it does**
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236
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237 Circos
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238
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239 Manual documentation available at the http://circos.ca/
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240
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241
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242 **Example of link segdup file**
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243
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244 segdup file::
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245
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246 1 hs1 1077096 1078746 color=red
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247 1 hs1 1080923 1082805 color=red
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248 2 hs1 1137684 1137961 color=red
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249 2 hs3 1138138 1138423 color=red
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250 3 hs11 1169417 1170000 color=red
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251 3 hs11 1170025 1170975 color=red
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252 4 hs11 1222480 1224271 color=green
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253 4 hs11 1223328 1225675 color=green
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254 5 hs12 1223336 1225812 color=grey
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255 5 hs13 1224709 1227633 color=grey
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256 6 hs11 1223621 1226460 color=red
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257 6 hs11 1224918 1227633 color=red
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258 7 hs11 1399510 1401513 color=white
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259 7 hs11 1401628 1403697 color=white
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260 8 hs15 1652045 1653746 color=red
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261 8 hs15 1657167 1658940 color=red
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262 9 hs11 165333 165887 color=white
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263 9 hs11 165981 168016 color=white
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264 10 hs11 1702700 1702841 color=red
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265 10 hs11 1702903 1703057 color=red
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266 11 hs11 1912272 1915186 color=white
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267 11 hs11 1937111 1939824 color=white
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268 12 hs11 1983211 1983355 color=red
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269 12 hs11 1983591 1983748 color=red
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270 13 hs11 2913657 2913898 color=white
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271 13 hs11 2914048 2914341 color=white
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272 14 hs11 3090593 3090749 color=purple
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273 14 hs11 3090709 3090864 color=purple
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274 15 hs21 3466365 3466434 color=red
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275 15 hs21 3466554 3466620 color=red
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276 16 hsX 3603073 3603321 color=white
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277 16 hsX 3603295 3603520 color=white
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278
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279
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280
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281 -----
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282
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283 .. class:: infomark
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284
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285 Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of Circos.
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286
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287
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288 </help>
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289
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290 </tool>
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