Mercurial > repos > dereeper > haplophyle
annotate Haplophyle.xml @ 2:d6281dc90e20 draft default tip
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date | Wed, 09 Jun 2021 16:54:15 +0000 |
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1 <tool id="haplophyle" name="Haplophyle" version="1.0.0"> |
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2 |
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3 <!-- [REQUIRED] Tool description displayed after the tool name --> |
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4 <description>Generates haplotype network</description> |
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5 |
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> |
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7 <requirements> |
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8 <requirement type="binary">perl</requirement> |
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9 <requirement type="package" version="1.6.924">perl-bioperl</requirement> |
2 | 10 <requirement type="package" version="8.0.112">java-jdk</requirement> |
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11 </requirements> |
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12 |
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13 |
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14 <!-- [STRONGLY RECOMMANDED] Exit code rules --> |
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15 <stdio> |
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16 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> |
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17 <exit_code range="1:" level="fatal" /> |
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18 </stdio> |
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19 |
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20 <!-- [REQUIRED] The command to execute --> |
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21 <command interpreter="perl"> |
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22 Haplophyle.sh $input $fileout $dotfile $filelog |
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23 #if str( $color.choice ) == "yes": |
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24 $color.input2 $color.groups |
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25 #end if |
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26 </command> |
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27 <!-- [REQUIRED] Input files and tool parameters --> |
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28 <inputs> |
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29 <param name="input" type="data" format="fasta" optional="false" label="Haplotype sequences in Fasta" /> |
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30 <conditional name="color"> |
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31 <param name="choice" type="boolean" truevalue="yes" falsevalue="no" label="Group colorization?"/> |
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32 <when value="no"> |
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33 </when> |
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34 <when value="yes"> |
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35 <param name="input2" type="data" format="txt" optional="true" label="Haplotype sequences and individuals carrying the haplotype" help="See example below"/> |
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36 <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Semicolon separated file (ind;group)"/> |
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37 </when> |
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38 </conditional> |
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39 </inputs> |
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40 |
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41 <!-- [REQUIRED] Output files --> |
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42 <outputs> |
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43 <data name="fileout" format="json" label="JSON for Cytoscape" /> |
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44 <data name="dotfile" format="txt" label="Dot file" /> |
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45 <data name="filelog" format="txt" label="Logfile" /> |
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46 </outputs> |
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47 |
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48 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> |
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49 <tests> |
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50 <!-- [HELP] Test files have to be in the ~/test-data directory --> |
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51 <test> |
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52 <param name="input" value="haplotype.fasta" /> |
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53 <conditional name="color"> |
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54 <param name="choice" value="yes" /> |
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55 <param name="input2" value="haplotype.txt" /> |
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56 <!--param name="groups" value="" /--> |
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57 </conditional> |
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58 <output name="fileout" file="output.json" compare="sim_size" delta="0"/> |
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59 <output name="dotfile" file="dotfile.txt" compare="sim_size" delta="0"/> |
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60 </test> |
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61 <test> |
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62 <param name="input" value="haplotype.fasta" /> |
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63 <conditional name="color"> |
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64 <param name="choice" value="no" /> |
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65 </conditional> |
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66 <output name="fileout" file="output.json" compare="sim_size" delta="20" /> |
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67 <output name="dotfile" file="dotfile.txt" compare="sim_size" delta="0" /> |
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68 </test> |
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69 </tests> |
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70 |
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71 |
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72 <!-- [OPTIONAL] Help displayed in Galaxy --> |
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73 <help><![CDATA[ |
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74 |
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75 .. class:: infomark |
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76 |
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77 **Authors** Gautier Sarah : Haplophyle_ |
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78 |
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79 .. _Haplophyle: http://haplophyle.cirad.fr/Haplophyle/ |
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80 |
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81 .. class:: infomark |
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82 |
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83 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) |
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84 |
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85 .. class:: infomark |
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86 |
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87 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
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88 |
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89 --------------------------------------------------- |
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90 |
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91 ================ |
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92 Haplophyle |
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93 ================ |
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94 |
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95 ----------- |
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96 Description |
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97 ----------- |
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98 |
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99 | Create haplotype network from haplotype sequences |
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100 |
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101 ---------- |
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102 Input file |
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103 ---------- |
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104 |
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105 Haplotype fasta file |
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106 Haplotype fasta file with haplotype sequences and proportion |
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107 Haplotype sequences and their individuals |
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108 Haplotype sequences and list of individuals holding the haplotype |
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109 |
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110 Groups |
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111 |
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112 ------------ |
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113 Output files |
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114 ------------ |
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115 |
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116 JSON file for Cytoscape |
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117 Dot file |
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118 Log file |
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119 |
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120 --------------------------------------------------- |
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121 |
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122 --------------- |
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123 Working example |
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124 --------------- |
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125 |
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126 Input files |
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127 =========== |
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128 |
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129 Haplotype fasta file |
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130 ---------------------------- |
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131 |
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132 :: |
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133 |
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134 >haplo1|1 |
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135 AGAGGCCCATT |
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136 >haplo2|1 |
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137 CGAGGTCCATT |
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138 >haplo3|1 |
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139 CGGAGCCCATT |
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140 >haplo4|2 |
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141 AGAGGTCTATT |
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142 >haplo5|1 |
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143 CGAGGTCTATT |
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144 >haplo6|7 |
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145 AGAGGTCCATT |
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146 >haplo7|3 |
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147 CAAGATCCATC |
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148 >haplo8|1 |
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149 CGAGGTTCATT |
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150 >haplo9|1 |
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151 CGGAGCCCGTT |
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152 >haplo10|1 |
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153 CGAGGCCCATT |
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154 >haplo11|1 |
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155 AGAGGTTCATT |
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156 >haplo12|38 |
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157 CAAGGTCCATT |
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158 >haplo13|3 |
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159 CAAGGTCCACT |
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160 >haplo14|1 |
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161 AGGAGCCCATT |
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162 |
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163 |
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164 Haplotype sequences and their individuals |
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165 ---------------------------------------------- |
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166 |
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167 :: |
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168 |
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169 haplo4:2:RS10_1,RS10_2, |
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170 GAGTGGGTTGCTTCCTTGCGTAGCCATCCGCCAACGACTGT |
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171 haplo5:2:RC3_1,RC3_2, |
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172 AGGTATACTGCCTGCTCGCGTAGTCAGCCGCCGACGGCTGG |
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173 haplo6:2:RS8_1,RS8_2, |
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174 GAGTGGGTTGCTTCCTTGCGTAGCCATCCACCAACGACTGT |
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175 haplo7:2:sativa_1,sativa_2, |
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176 GAGTGGGCTGCTTCCTCGCGTAGTCAGCCGCCGACAGCTGG |
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177 |
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178 |
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179 |
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180 Output files |
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181 ============ |
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182 |
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183 output.json |
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184 ---------------------------- |
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185 |
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186 :: |
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187 |
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188 {"elements": {"nodes": [{ "data": { "id": "MV1", "width": 0.1} }, |
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189 { "data": { "id": "MV2", "width": 0.1} }, |
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190 { "data": { "id": "MV3", "width": 0.1} }, |
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191 { "data": { "id": "haplo6", "width": 0.8 } }, |
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192 { "data": { "id": "haplo7", "width": 0.8 } }, |
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193 { "data": { "id": "haplo8", "width": 0.8 } }], |
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194 "edges": [ |
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195 { "data": { "id": "haplo4MV1", "weight": 1, "source": "haplo4", "target": "MV1"} }, |
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196 { "data": { "id": "haplo3haplo4", "weight": 1, "source": "haplo3", "target": "haplo4"} }, |
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197 { "data": { "id": "haplo5MV3", "weight": 1, "source": "haplo5", "target": "MV3"} }, |
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198 { "data": { "id": "MV1MV2", "weight": 1, "source": "MV1", "target": "MV2"} }, |
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199 { "data": { "id": "haplo8MV3", "weight": 1, "source": "haplo8", "target": "MV3"} }]}} |
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200 |
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201 |
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202 dotfile.txt |
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203 ---------------------------- |
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204 |
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205 :: |
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206 |
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207 graph G { |
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208 overlap="scale"; |
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209 outputMode="nodesfirst"; |
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210 MV1 [shape="circle", color="red", width=0.1, height=0.1,fixedsize=true]; |
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211 MV2 [shape="circle", color="red", width=0.1, height=0.1,fixedsize=true]; |
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212 haplo2 [shape="circle",style="filled", color="green" , imagescale="both", width=0.8, height=0.8,fixedsize=true]; |
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213 haplo4 [shape="circle",style="filled", color="green" , imagescale="both", width=0.8, height=0.8,fixedsize=true]; |
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214 haplo8 [shape="circle",style="filled", color="green" , imagescale="both", width=0.8, height=0.8,fixedsize=true]; |
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215 haplo7 -- MV2 [len=0.2]; |
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216 haplo1 -- haplo2 [len=0.2]; |
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217 haplo4 -- MV1 [len=0.2]; |
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218 MV2 -- MV3 [len=0.6]; |
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219 haplo5 -- MV3 [len=0.8]; |
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220 haplo8 -- MV3 [len=1,label="length: 24.0",color="red"]; |
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221 } |
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222 |
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223 |
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224 |
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225 |
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226 ]]></help> |
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227 |
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228 </tool> |