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1 <tool id="sniplay_mdsplot" name="MDS plot" version="1.1.1">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> IBS matrix / multi-dimensional scaling</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="0.1.13">plink</requirement>
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10 </requirements>
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11
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12 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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13 <version_command>
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14 <!--
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15 tool_binary -v
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16 -->
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17 </version_command>
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18
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19 <!-- [REQUIRED] The command to execute -->
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20 <command interpreter="bash">
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21 mdsplot.sh $fileped $filemap $fileout_label $fileout_matrix $fileout_plot $fileout_log
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22 </command>
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23
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24 <!-- [REQUIRED] Input files and tool parameters -->
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25 <inputs>
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26 <param name="fileped" type="data" format="txt" optional="false" label="PED input" />
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27 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/>
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28 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
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29 </inputs>
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30
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31 <!-- [REQUIRED] Output files -->
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32 <outputs>
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33 <data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" />
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34 <data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" />
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35 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
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36 </outputs>
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37
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38 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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39 <stdio>
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40 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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41 <exit_code range="1:" level="fatal" />
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42 </stdio>
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43
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44 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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45 <tests>
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46 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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47
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48 <test>
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49 <param name="fileped" value="input.ped" />
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50 <param name="filemap" value="input.map" />
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51 <output name="fileout_matrix" file="output.ibs_matrix.txt" />
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52 <output name="fileout_plot" file="output.mds_plot.txt" />
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53 <output name="fileout_log" file="output.log" />
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54 </test>
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55
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56 <!-- [HELP] Multiple tests can be defined with different parameters -->
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57 <!--
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58 <test>
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59 </test>
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60 -->
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61 </tests>
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62
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63 <!-- [OPTIONAL] Help displayed in Galaxy -->
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64 <help>
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65
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66 .. class:: infomark
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67
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68 **Authors**
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69
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70 ---------------------------------------------------
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71
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72 .. class:: infomark
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73
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74 **Please cite** If you use this tool, please cite dereeper et al. 2015 in prep.
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75
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76 ---------------------------------------------------
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77
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78 ========
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79 MDS plot
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80 ========
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81
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82 -----------
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83 Description
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84 -----------
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85
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86 Compute an IBS matrix and a multi-dimensional scaling.
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87
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88
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89 -----------------
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90 Workflow position
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91 -----------------
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92
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93 **Upstream tools**
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94
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95 =========== ========================== =======
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96 Name output file(s) format
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97 =========== ========================== =======
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98 =========== ========================== =======
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99
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100
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101 **Downstream tools**
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102
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103 =========== ========================== =======
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104 Name output file(s) format
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105 =========== ========================== =======
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106 =========== ========================== =======
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107
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108
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109 ----------
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110 Input file
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111 ----------
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112
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113 PED file
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114
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115 MAP file
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116 4 columns tabular file: chromosome, snp id, genetic distance, bp position
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117
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118
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119 ----------
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120 Parameters
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121 ----------
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122
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123 Output name
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124 Output base name for the ouput files
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125
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126
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127 ------------
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128 Output files
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129 ------------
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130
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131 Output_name.ibs_matrix.txt
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132 Tabular file with IBS matrix
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133
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134 Output_name.mds_plot.txt
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135 File to construct mds plot
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136
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137 Output_name.log
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138 Log file
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139
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140
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141 ---------------------------------------------------
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142
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143 ---------------
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144 Working example
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145 ---------------
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146
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147 Input files
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148 ===========
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149
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150 PED file
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151 -----------
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152
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153 ::
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154
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155 IRAT112 1 0 0 1 1 1 1 4 4 ...
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156 IAC25 1 0 0 1 1 1 1 4 4 ...
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157 CIRAD409 1 0 0 1 1 3 3 1 1 ...
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158
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159
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160 MAP file
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161 -----------
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162
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163 ::
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164
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165 Chr1 Chr1:4299 0 4299
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166 Chr1 Chr1:26710 0 26710
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167 Chr1 Chr1:56184 0 56184
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168 Chr1 Chr1:93272 0 93272
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169
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170
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171
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172 Parameters
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173 ==========
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174
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175 Output name -> densities
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176
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177
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178 Output files
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179 ============
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180
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181 densities.ibs_matrix.txt
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182 ------------------------
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183
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184 ::
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185
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186 Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ...
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187 IRAT112 1 0.93691 0.937407 0.734724 0.943368 ...
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188 IAC25 0.93691 1 0.958768 0.723299 0.965723 ...
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189
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190
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191 densities.mds_plot.txt
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192 ----------------------
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193
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194 ::
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195
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196 IRAT112 -0.0969382 0.0376036
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197 IAC25 -0.0918126 0.0501177
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198
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199
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200
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201 </help>
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202
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203 </tool>
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