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1 <tool id="rest_tool" name="Fetch Data from pubchem" version="0.1.0">
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2 <description>Fetch pubchem data</description>
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3 <version_command>echo "0.1.0"</version_command>
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4 <requirements>
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5 <requirement type="set_environment">REST_TOOL_SCRIPT_PATH</requirement>
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6 </requirements>
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7 <macros>
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8 <import>rest_tool_macros.xml</import>
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9 </macros>
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10 <command interpreter="python">
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11 #if $choose_action.action == 'search':
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12 rest_tool_search.py --type $choose_action.input_type_search --name $choose_action.search_name --outfile $output
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13
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14 #elif $choose_action.action == 'specific_data':
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15 rest_tool.py
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16 #if $choose_action.field_or_file1.field_or_file1 == 'field':
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17 --id $choose_action.field_or_file1.id1
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18 #else:
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19 --id-file $choose_action.field_or_file1.file_ids_1
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20 #end if
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21 --type $choose_action.choose_acs.input_type
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22
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23 #if $choose_action.choose_acs.input_type == 'assay':
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24 --operation $choose_action.choose_acs.operation_assay.operation_assay
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25 #if $choose_action.choose_acs.operation_assay.operation_assay == 'property':
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26 --property-value $choose_action.choose_acs.operation_assay.property_assay
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27 #elif $choose_action.choose_acs.operation_assay.operation_assay == 'aids':
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28 --id-type $choose_action.choose_acs.operation_assay.aids_type_assay
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29 #elif $choose_action.choose_acs.operation_assay.operation_assay == 'cids':
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30 --id-type $choose_action.choose_acs.operation_assay.cids_type_assay
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31 #elif $choose_action.choose_acs.operation_assay.operation_assay == 'sids':
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32 --id-type $choose_action.choose_acs.operation_assay.sids_type_assay
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33 #end if
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34 #elif $choose_action.choose_acs.input_type == 'compound':
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35 --operation $choose_action.choose_acs.operation_compound.operation_compound
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36 #if $choose_action.choose_acs.operation_compound.operation_compound == 'property':
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37 --property-value $choose_action.choose_acs.operation_compound.property_compound
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38 #elif $choose_action.choose_acs.operation_compound.operation_compound == 'aids':
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39 --id-type $choose_action.choose_acs.operation_compound.aids_type_compound
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40 #elif $choose_action.choose_acs.operation_compound.operation_compound == 'cids':
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41 --id-type $choose_action.choose_acs.operation_compound.cids_type_compound
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42 #elif $choose_action.choose_acs.operation_compound.operation_compound == 'sids':
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43 --id-type $choose_action.choose_acs.operation_compound.sids_type_compound
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44 #end if
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45 #else:
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46 --operation $choose_action.choose_acs.operation_substance.operation_substance
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47 #if $choose_action.choose_acs.operation_substance.operation_substance == 'property':
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48 --property-value $choose_action.choose_acs.operation_substance.property_substance
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49 #elif $choose_action.choose_acs.operation_substance.operation_substance == 'aids':
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50 --id-type $choose_action.choose_acs.operation_substance.aids_type_substance
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51 #elif $choose_action.choose_acs.operation_substance.operation_substance == 'cids':
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52 --id-type $choose_action.choose_acs.operation_substance.cids_type_substance
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53 #elif $choose_action.choose_acs.operation_substance.operation_substance == 'sids':
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54 --id-type $choose_action.choose_acs.operation_substance.sids_type_substance
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55 #end if
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56 #end if
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57 --outfile $output
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58 #elif $choose_action.action == 'compounds_for_assay':
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59 rest_tool_comp_for_assay.py
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60 #if $choose_action.field_or_file2.field_or_file2 == 'field':
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61 --aid $choose_action.field_or_file2.id2
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62 #else:
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63 --aid-file $choose_action.field_or_file2.file_ids_2
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64 #end if
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65 --outfile $output
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66 #elif $choose_action.action == 'assays_by_activity_or_target':
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67 rest_tool_assay_by_activity_or_target.py
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68 #if $choose_action.activity_or_target.activity_or_target == 'activity':
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69 --activity $choose_action.activity_or_target.activity
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70 #else:
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71 --target $choose_action.activity_or_target.target_id
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72 --target-type $choose_action.activity_or_target.target_identifier_type
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73 #end if
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74 --outfile $output
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75
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76 #end if
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77 </command>
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78
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79 <inputs>
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80 <conditional name="choose_action">
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81 <param name="action" multiple="false" type="select" label="Choose action">
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82 <option value="search">Search for Assay/Compound/Substance</option>
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83 <option value="specific_data">Get Data for specific Assay/Compound/Substance</option>
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84 <option value="compounds_for_assay">Get all compound IDs given BioAssay IDs</option>
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85 <option value="assays_by_activity_or_target">Get BioAssay IDs given activity/target</option>
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86 </param>
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87 <when value="search">
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88 <param name="input_type_search" multiple="false" type="select" label="Search for">
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89 <option value="assay">BioAssay</option>
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90 <option value="compound">Compound</option>
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91 <option value="substance">Substance</option>
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92 </param>
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93 <param name="input_type" multiple="false" type="select" label="Search By">
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94 <option value="name">Name</option>
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95 </param>
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96 <param format="txt" name="search_name" type="text" label="Enter the Name" />
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97 </when>
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98 <when value="specific_data">
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99 <conditional name="field_or_file1">
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100 <param name="field_or_file1" multiple="false" type="select" label="Specify the ID by">
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101 <option value="field" selected="True">Textfield</option>
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102 <option value="file">File</option>
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103 </param>
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104 <when value="field">
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105 <param format="txt" name="id1" type="text" label="Enter the ID(s)" />
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106 </when>
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107 <when value="file">
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108 <param format="txt,csv" name="file_ids_1" type="data" label="Give the file" />
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109 </when>
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110 </conditional>
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111 <conditional name="choose_acs">
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112 <param name="input_type" multiple="false" type="select" label="Input Type">
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113 <option value="assay">BioAssay</option>
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114 <option value="compound">Compound</option>
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115 <option value="substance">Substance</option>
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116 </param>
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117
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118 <when value="assay">
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119 <conditional name="operation_assay">
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120 <param name="operation_assay" type="select" multiple="false" label="Operation">
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121 <expand macro="aid_cid_sid" />
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122 <option value="record">Record</option>
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123 <option value="classification">Classification</option>
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124 <option value="property">Property</option>
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125 <option value="description">Discription</option>
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126 <option value="summary">Summary</option>
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127 </param>
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128 <when value="property">
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129 <param name="property_assay" label="Specify Property" type="text" />
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130 </when>
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131 <when value="aids">
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132 <param name="aids_type_assay" multiple="false" type="select" label="AID Type">
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133 <expand macro="aids_when_options" />
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134 </param>
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135 </when>
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136 <when value="cids">
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137 <param name="cids_type_assay" multiple="false" type="select" label="CID Type">
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138 <expand macro="aids_when_options" />
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139
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140 </param>
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141 </when>
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142 <when value="sids">
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143 <param name="sids_type_assay" multiple="false" type="select" label="SID Type">
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144 <expand macro="aids_when_options" />
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145 <option value="doseresponse">doseresponse</option>
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146 </param>
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147 </when>
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148 </conditional>
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149 </when>
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150 <when value="compound">
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151 <conditional name="operation_compound">
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152 <param name="operation_compound" type="select" multiple="false" label="Operation">
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153 <expand macro="aid_cid_sid" />
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154 <expand macro="option_compound_substance" />
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155 <option value="property">Property</option>
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156 </param>
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157 <when value="property">
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158 <param name="property_compound" label="Specify Property" type="text" />
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159 </when>
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160 <when value="aids">
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161 <param name="aids_type_compound" multiple="false" type="select" label="AID Type">
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162 <expand macro="aids_when_options" />
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163 </param>
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164 </when>
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165 <when value="sids">
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166 <param name="sids_type_compound" multiple="false" type="select" label="SID Type">
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167
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168 <expand macro="cid_sid_type_options" />
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169 </param>
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170 </when>
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171 <when value="cids">
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172 <param name="cids_type_compound" multiple="false" type="select" label="CID Type">
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173 <expand macro="cid_cid_type_options" />
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174 </param>
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175 </when>
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176 </conditional>
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177 </when>
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178 <when value="substance">
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179 <conditional name="operation_substance">
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180 <param name="operation_substance" type="select" multiple="false" label="Operation">
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181 <expand macro="aid_cid_sid" />
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182 <expand macro="option_compound_substance" />
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183 </param>
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184 <when value="property">
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185 <param name="property_substance" label="Specify Property" type="text" />
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186 </when>
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187 <when value="aids">
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188 <param name="aids_type_substance" multiple="false" type="select" label="AID Type">
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189 <expand macro="aids_when_options" />
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190 </param>
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191 </when>
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192 <when value="cids">
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193 <param name="cids_type_substance" multiple="false" type="select" label="CID Type">
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194 <expand macro="sid_cid_type_options" />
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195 </param>
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196 </when>
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197 <when value="sids">
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198 <param name="sids_type_substance" multiple="false" type="select" label="SID Type">
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199 <expand macro="sid_sid_type_options" />
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200 </param>
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201 </when>
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202
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203 </conditional>
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204 </when>
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205 </conditional>
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206 </when>
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207 <!-- second option -->
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208 <when value="compounds_for_assay">
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209 <conditional name="field_or_file2">
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210 <param name="field_or_file2" multiple="false" type="select" label="Specify the ID by">
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211 <option value="field">Textfield</option>
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212 <option value="file">File</option>
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213 </param>
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214 <when value="field">
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215 <param format="txt" name="id2" type="text" label="Enter the ID(s)" />
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216 </when>
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217 <when value="file">
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218 <param format="txt,csv" name="file_ids_2" type="data" label="Give the file" />
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219 </when>
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220 </conditional>
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221 </when>
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222 <!-- third option -->
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223 <when value="assays_by_activity_or_target">
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224 <conditional name="activity_or_target">
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225 <param name="activity_or_target" multiple="false" type="select" label="Look for">
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226 <option value="target">Target</option>
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227 <option value="activity">Activity</option>
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228 </param>
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229 <when value="activity">
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230 <param format="txt" name="activity" type="text" label="Enter the activity" />
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231 </when>
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232
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233 <when value="target">
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234 <param name="target_identifier_type" multiple="false" type="select" label="Choose target identifier">
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235 <option value="gi">GI</option>
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236 <option value="geneid">Gene ID</option>
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237 <option value="genesymbol">Gene Symbol</option>
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238 </param>
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239 <param format="txt" name="target_id" type="text" label="Enter the target" />
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240 </when>
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241 </conditional>
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242 </when>
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243
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244 </conditional>
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245 </inputs>
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246 <outputs>
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247 <data format="csv" name="output" />
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248 </outputs>
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249 <tests>
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250 </tests>
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251 <help>
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252 **What it does**
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253
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254 This tool fetches data from pubchem
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255 </help>
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256 </tool>
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