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1 <tool id="hgv_ctdBatch" name="CTD" version="1.0.0">
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2 <description>analysis of chemicals, diseases, or genes</description>
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3
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4 <command interpreter="perl">
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5 ctd.pl $input $numerical_column $inType.inputType
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6 #if $inType.inputType == "disease"
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7 $inType.report ANY
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8 #else if $inType.reportType.report == "cgixns"
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9 $inType.reportType.report $inType.reportType.actType
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10 #else
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11 $inType.reportType.report ANY
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12 #end if
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13 $out_file1
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14 </command>
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15
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16 <inputs>
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17 <param name="input" type="data" format="tabular" label="Dataset" />
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18 <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" />
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19 <conditional name="inType">
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20 <param name="inputType" label="Identifier type" type="select">
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21 <option value="chem">Chemicals (MeSH names, synonyms or accession IDs, or CAS RNs)</option>
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22 <option value="disease">Diseases (MeSH or OMIM names, synonyms or accession IDs)</option>
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23 <option value="gene" selected="true">Genes (NCBI official symbols or accession IDs)</option>
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24 </param>
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25 <when value="chem">
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26 <conditional name='reportType'>
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27 <param name="report" label="Data to extract" type="select">
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28 <option value="cgixns">Curated chemical-gene interactions</option>
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29 <option value="genes">Curated gene associations</option>
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30 <option value="pathways">Pathway associations</option>
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31 <option value="diseases" selected="true">All disease relationships</option>
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32 <option value="diseases_direct"> Direct disease relationships only</option>
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33 <option value="diseases_inferred"> Inferred disease relationships only</option>
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34 <option value="go">All GO associations</option>
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35 <option value="go_p"> GO biological Processes only</option>
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36 <option value="go_f"> GO molecular Functions only</option>
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37 <option value="go_c"> GO cellular Components only</option>
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38 </param>
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39 <when value="genes">
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40 <!-- do nothing -->
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41 </when>
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42 <when value="pathways">
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43 <!-- do nothing -->
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44 </when>
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45 <when value="diseases">
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46 <!-- do nothing -->
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47 </when>
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48 <when value="diseases_direct">
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49 <!-- do nothing -->
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50 </when>
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51 <when value="diseases_inferred">
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52 <!-- do nothing -->
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53 </when>
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54 <when value="go">
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55 <!-- do nothing -->
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56 </when>
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57 <when value="go_p">
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58 <!-- do nothing -->
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59 </when>
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60 <when value="go_f">
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61 <!-- do nothing -->
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62 </when>
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63 <when value="go_c">
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64 <!-- do nothing -->
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65 </when>
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66 <when value="cgixns">
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67 <param name="actType" label="Interaction type" type="select">
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68 <option value="ANY">ANY</option>
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69 <option value="abundance">abundance</option>
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70 <option value="activity">activity</option>
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71 <option value="binding">binding</option>
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72 <option value="cotreatment">cotreatment</option>
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73 <option value="expression">expression</option>
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74 <option value="folding">folding</option>
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75 <option value="localization">localization</option>
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76 <option value="metabolic processing">metabolic processing</option>
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77 <option value="acetylation">- acetylation</option>
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78 <option value="acylation">- acylation</option>
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79 <option value="alkylation">- alkylation</option>
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80 <option value="amination">- amination</option>
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81 <option value="carbamoylation">- carbamoylation</option>
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82 <option value="carboxylation">- carboxylation</option>
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83 <option value="chemical synthesis">- chemical synthesis</option>
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84 <option value="degradation">- degradation</option>
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85 <option value="cleavage"> - cleavage</option>
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86 <option value="hydrolysis"> - hydrolysis</option>
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87 <option value="ethylation">- ethylation</option>
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88 <option value="glutathionylation">- glutathionylation</option>
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89 <option value="glycation">- glycation</option>
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90 <option value="glycosylation">- glycosylation</option>
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91 <option value="N-linked glycosylation"> - N-linked glycosylation</option>
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92 <option value="O-linked glycosylation"> - O-linked glycosylation</option>
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93 <option value="glucuronidation"> - glucuronidation</option>
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94 <option value="hydroxylation">- hydroxylation</option>
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95 <option value="lipidation">- lipidation</option>
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96 <option value="farnesylation"> - farnesylation</option>
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97 <option value="geranolyation"> - geranolyation</option>
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98 <option value="myristolylation"> - myristolylation</option>
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99 <option value="palmitoylation"> - palmitoylation</option>
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100 <option value="prenylation"> - prenylation</option>
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101 <option value="methylation">- methylation</option>
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102 <option value="nitrosation">- nitrosation</option>
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103 <option value="nucleotidylation">- nucleotidylation</option>
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104 <option value="oxidation">- oxidation</option>
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105 <option value="phosphorylation">- phosphorylation</option>
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106 <option value="reduction">- reduction</option>
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107 <option value="ribosylation">- ribosylation</option>
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108 <option value="ADP-ribosylation"> - ADP-ribosylation</option>
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109 <option value="sulfation">- sulfation</option>
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110 <option value="sumoylation">- sumoylation</option>
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111 <option value="ubiquitination">- ubiquitination</option>
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112 <option value="mutagenesis">mutagenesis</option>
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113 <option value="reaction">reaction</option>
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114 <option value="response to chemical">response to chemical</option>
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115 <option value="splicing">splicing</option>
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116 <option value="stability">stability</option>
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117 <option value="transport">transport</option>
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118 <option value="secretion">- secretion</option>
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119 <option value="export"> - export</option>
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120 <option value="uptake">- uptake</option>
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121 <option value="import"> - import</option>
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122 </param>
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123 </when>
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124 </conditional>
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125 </when>
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126 <when value="disease">
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127 <param name="report" label="Data to extract" type="select">
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128 <option value="chems">Chemical associations</option>
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129 <option value="chems_direct">Chemical associations direct relationships only</option>
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130 <option value="chems_inferred">Chemical associations inferred relationships only</option>
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131 <option value="genes">Curated gene associations</option>
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132 <option value="pathways">Pathway associations</option>
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133 </param>
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134 </when>
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135 <when value="gene">
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136 <conditional name='reportType'>
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137 <param name="report" label="Data to extract" type="select">
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138 <option value="cgixns">Curated chemical-gene interactions</option>
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139 <option value="chems">Curated chemical associations</option>
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140 <option value="pathways">Pathway associations</option>
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141 <option value="diseases" selected="true">All disease relationships</option>
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142 <option value="diseases_direct"> Direct disease relationships only</option>
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143 <option value="diseases_inferred"> Inferred disease relationships only</option>
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144 <option value="go">All GO associations</option>
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145 <option value="go_p"> GO biological Processes only</option>
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146 <option value="go_f"> GO molecular Functions only</option>
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147 <option value="go_c"> GO cellular Components only</option>
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148 </param>
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149 <when value="chems">
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150 <!-- do nothing -->
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151 </when>
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152 <when value="pathways">
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153 <!-- do nothing -->
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154 </when>
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155 <when value="diseases">
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156 <!-- do nothing -->
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157 </when>
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158 <when value="diseases_direct">
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159 <!-- do nothing -->
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160 </when>
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161 <when value="diseases_inferred">
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162 <!-- do nothing -->
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163 </when>
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164 <when value="go">
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165 <!-- do nothing -->
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166 </when>
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167 <when value="go_p">
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168 <!-- do nothing -->
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169 </when>
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170 <when value="go_f">
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171 <!-- do nothing -->
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172 </when>
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173 <when value="go_c">
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174 <!-- do nothing -->
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175 </when>
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176 <when value="cgixns">
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177 <param name="actType" label="Interaction type" type="select">
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178 <option value="ANY">ANY</option>
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179 <option value="abundance">abundance</option>
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180 <option value="activity">activity</option>
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181 <option value="binding">binding</option>
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182 <option value="cotreatment">cotreatment</option>
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183 <option value="expression">expression</option>
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184 <option value="folding">folding</option>
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185 <option value="localization">localization</option>
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186 <option value="metabolic processing">metabolic processing</option>
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187 <option value="acetylation">- acetylation</option>
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188 <option value="acylation">- acylation</option>
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189 <option value="alkylation">- alkylation</option>
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190 <option value="amination">- amination</option>
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191 <option value="carbamoylation">- carbamoylation</option>
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192 <option value="carboxylation">- carboxylation</option>
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193 <option value="chemical synthesis">- chemical synthesis</option>
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194 <option value="degradation">- degradation</option>
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195 <option value="cleavage"> - cleavage</option>
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196 <option value="hydrolysis"> - hydrolysis</option>
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197 <option value="ethylation">- ethylation</option>
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198 <option value="glutathionylation">- glutathionylation</option>
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199 <option value="glycation">- glycation</option>
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200 <option value="glycosylation">- glycosylation</option>
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201 <option value="N-linked glycosylation"> - N-linked glycosylation</option>
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202 <option value="O-linked glycosylation"> - O-linked glycosylation</option>
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203 <option value="glucuronidation"> - glucuronidation</option>
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204 <option value="hydroxylation">- hydroxylation</option>
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205 <option value="lipidation">- lipidation</option>
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206 <option value="farnesylation"> - farnesylation</option>
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207 <option value="geranolyation"> - geranolyation</option>
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208 <option value="myristolylation"> - myristolylation</option>
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209 <option value="palmitoylation"> - palmitoylation</option>
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210 <option value="prenylation"> - prenylation</option>
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211 <option value="methylation">- methylation</option>
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212 <option value="nitrosation">- nitrosation</option>
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213 <option value="nucleotidylation">- nucleotidylation</option>
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214 <option value="oxidation">- oxidation</option>
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215 <option value="phosphorylation">- phosphorylation</option>
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216 <option value="reduction">- reduction</option>
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217 <option value="ribosylation">- ribosylation</option>
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218 <option value="ADP-ribosylation"> - ADP-ribosylation</option>
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219 <option value="sulfation">- sulfation</option>
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220 <option value="sumoylation">- sumoylation</option>
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221 <option value="ubiquitination">- ubiquitination</option>
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222 <option value="mutagenesis">mutagenesis</option>
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223 <option value="reaction">reaction</option>
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224 <option value="response to chemical">response to chemical</option>
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225 <option value="splicing">splicing</option>
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226 <option value="stability">stability</option>
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227 <option value="transport">transport</option>
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228 <option value="secretion">- secretion</option>
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229 <option value="export"> - export</option>
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230 <option value="uptake">- uptake</option>
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231 <option value="import"> - import</option>
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232 </param>
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233 </when>
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234 </conditional>
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235 </when>
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236 </conditional>
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237 </inputs>
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238
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239 <outputs>
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240 <data format="tabular" name="out_file1" />
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241 </outputs>
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242
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243 <!-- broken for now. will be fixed soon.
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244 <tests>
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245 <test>
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246 <param name="input" ftype="tabular" value="ctdBatchInput.txt" />
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247 <param name="numerical_column" value="1" />
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248 <param name="inputType" value="gene" />
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249 <param name="report" value="diseases" />
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250 <output name="out_file1" file="ctdBatchOut.txt" />
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251 </test>
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252 </tests>
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253 -->
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254
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255 <help>
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256 **Dataset formats**
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257
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258 The input and output datasets are tabular_.
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259 (`Dataset missing?`_)
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260
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261 .. _tabular: ./static/formatHelp.html#tab
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262 .. _Dataset missing?: ./static/formatHelp.html
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263
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264 -----
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265
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266 **What it does**
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267
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268 This tool extracts data related to the provided list of identifiers
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269 from the Comparative Toxicogenomics Database (CTD). The fields
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270 extracted vary with the type of data requested; the first row
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271 of the output identifies the columns.
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272
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273 For the curated chemical-gene interactions, you can also choose the
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274 interaction type from the search-and-select box. The choices that
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275 start with '-' are a subset of a choice above them; you can chose
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276 either the general interaction type or a more specific one.
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277
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278 Website: http://ctd.mdibl.org/
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279
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280 -----
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281
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282 **Examples**
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283
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284 - input data file:
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285 HBB
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286
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287 - select Column = c1, Identifier type = Genes, and Data to extract = All disease relationships
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288
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289 - output file::
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290
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291 #Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs
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292 hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900
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293 hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741
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294 etc.
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295
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296 Another example:
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297
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298 - same input file:
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299 HBB
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300
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301 - select Column = c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY
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302
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303 - output file::
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304
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305 #Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs
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306 hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347
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307 hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499
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308 etc.
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309
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310 -----
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311
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312 **Reference**
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313
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314 Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. (2009)
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315 Comparative Toxicogenomics Database: a knowledgebase and discovery tool for
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316 chemical-gene-disease networks.
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317 Nucleic Acids Res. 37(Database issue):D786-92. Epub 2008 Sep 9.
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318
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319 </help>
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320 </tool>
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