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1 <tool id="draw_circos" name="draw_circos" version="0.1">
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2 <description> : Draw circos figure</description>
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3 <requirements>
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4 <requirement type="binary">circos</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command>
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10 source $__tool_directory__/include_scaffremodler.sh ;
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11 python $__tool_directory__/draw_circos.py
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12 --config $config
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13 --draw $draw
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14 --cov $cov
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15 --scaff $scaff
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16 --discord $discord
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17 --frf $frf
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18 --ff $ff
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19 --rr $rr
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20 --ins $ins
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21 --delet $delet
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22 --chr_rr $chr_rr
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23 --chr_rf $chr_rf
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24 --chr_fr $chr_fr
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25 --chr_ff $chr_ff
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26 --read_fr $read_fr
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27 --read_rf $read_rf
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28 --read_ff $read_ff
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29 --read_rr $read_rr
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30 --read_ins $read_ins
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31 --read_delet $read_delet
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32 --read_chr_rr $read_chr_rr
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33 --read_chr_rf $read_chr_rf
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34 --read_chr_fr $read_chr_fr
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35 --read_chr_ff $read_chr_ff
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36 --text $text
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37 --out $circos_file
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38
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39 </command>
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40 <inputs>
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41 <param name="config" type="data" label="The circos_conf file generated by conf4circos" />
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42 <param name="draw" type="text" value="all" label="Region to draw ('all' or potitions separated by ':' : chrX:start1:end1-chrY:start2:end2)" />
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43
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44 <param name="cov" type="select" label="Draw coverage layer">
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45 <option selected="true" value="y">y</option>
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46 <option value="n">n</option>
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47 </param>
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48
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49 <param name="scaff" type="select" label="Draw scaffold location layer">
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50 <option selected="true" value="y">y</option>
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51 <option value="n">n</option>
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52 </param>
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53
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54 <param name="discord" type="select" label="Draw discordant proportion layer">
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55 <option selected="true" value="y">y</option>
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56 <option value="n">n</option>
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57 </param>
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58
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59
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60 <param name="frf" type="select" label="Draw fr/rf discordant regions links">
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61 <option selected="true" value="y">y</option>
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62 <option value="n">n</option>
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63 </param>
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64
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65 <param name="ff" type="select" label="Draw ff discordant regions links">
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66 <option selected="true" value="y">y</option>
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67 <option value="n">n</option>
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68 </param>
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69
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70 <param name="rr" type="select" label="Draw rr discordant regions links">
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71 <option selected="true" value="y">y</option>
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72 <option value="n">n</option>
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73 </param>
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74
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75 <param name="ins" type="select" label="Draw ins discordant regions links">
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76 <option selected="true" value="y">y</option>
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77 <option value="n">n</option>
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78 </param>
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79
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80 <param name="delet" type="select" label="Draw delet discordant regions links">
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81 <option selected="true" value="y">y</option>
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82 <option value="n">n</option>
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83 </param>
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84
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85 <param name="chr_rf" type="select" label="Draw chr_rf discordant regions links">
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86 <option selected="true" value="y">y</option>
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87 <option value="n">n</option>
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88 </param>
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89
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90 <param name="chr_rr" type="select" label="Draw chr_rr discordant regions links">
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91 <option selected="true" value="y">y</option>
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92 <option value="n">n</option>
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93 </param>
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94
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95 <param name="chr_fr" type="select" label="Draw chr_fr discordant regions links">
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96 <option selected="true" value="y">y</option>
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97 <option value="n">n</option>
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98 </param>
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99 <param name="chr_ff" type="select" label="Draw chr_ff discordant regions links">
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100 <option selected="true" value="y">y</option>
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101 <option value="n">n</option>
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102 </param>
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103
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104
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105
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106 <param name="read_rf" type="select" label="Draw rf read links">
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107 <option selected="true" value="y">y</option>
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108 <option value="n">n</option>
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109 </param>
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110
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111 <param name="read_fr" type="select" label="Draw fr read links">
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112 <option selected="true" value="y">y</option>
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113 <option value="n">n</option>
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114 </param>
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115
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116 <param name="read_ff" type="select" label="Draw ff read links">
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117 <option selected="true" value="y">y</option>
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118 <option value="n">n</option>
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119 </param>
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120
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121 <param name="read_rr" type="select" label="Draw rr read links">
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122 <option selected="true" value="y">y</option>
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123 <option value="n">n</option>
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124 </param>
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125
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126 <param name="read_ins" type="select" label="Draw ins read links">
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127 <option selected="true" value="y">y</option>
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128 <option value="n">n</option>
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129 </param>
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130
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131 <param name="read_delet" type="select" label="Draw delet read links">
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132 <option selected="true" value="y">y</option>
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133 <option value="n">n</option>
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134 </param>
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135
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136 <param name="read_chr_rf" type="select" label="Draw chr_rf read links">
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137 <option selected="true" value="y">y</option>
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138 <option value="n">n</option>
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139 </param>
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140
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141 <param name="read_chr_rr" type="select" label="Draw chr_rr read links">
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142 <option selected="true" value="y">y</option>
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143 <option value="n">n</option>
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144 </param>
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145
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146 <param name="read_chr_fr" type="select" label="Draw chr_fr read links">
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147 <option selected="true" value="y">y</option>
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148 <option value="n">n</option>
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149 </param>
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150 <param name="read_chr_ff" type="select" label="Draw chr_ff read links">
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151 <option selected="true" value="y">y</option>
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152 <option value="n">n</option>
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153 </param>
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154
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155 <param name="text" type="select" label="Draw a text layer locating N regions">
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156 <option selected="true" value="y">y</option>
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157 <option value="n">n</option>
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158 </param>
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159
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160 <param name="prefix" type="text" label="Identifier for output" value="circos" />
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161 </inputs>
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162 <outputs>
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163 <data name="circos_file" format="png" label="${tool.name} : $prefix .png" />
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164 </outputs>
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165 <help>
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166
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167 **Overview**
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168
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169 -----
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170
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171 .. class:: infomark
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172
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173 **Galaxy integration** Martin Guillaume (CIRAD), Droc Gaetan (CIRAD).
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174
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175 .. class:: infomark
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176
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177 **Support** For any questions about Galaxy integration, please send an e-mail to galaxy-dev-southgreen@cirad.fr
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178
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179 .. class:: infomark
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180
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181 **Program encapsulated in Galaxy by South Green**
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182
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183 </help>
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184 <citations>
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185 <citation type="doi">10.1186/s12864-016-2579-4</citation>
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186 </citations>
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187 </tool> |
