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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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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description>Generates haplotype network</description>
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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>
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10 <requirement type="package" version="8.0.112">java-jdk</requirement>
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11 </requirements>
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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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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>