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6
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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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8
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9 <import>rest_tool_macro_advanced.xml</import>
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6
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10 </macros>
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11 <command interpreter="python">
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8
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12 #if $choose_action.action == 'specific_data':
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6
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13 rest_tool.py
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8
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14 #if $choose_action.field_or_file.field_or_file_select == 'field':
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15 --id $choose_action.field_or_file.id_value
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6
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16 #else:
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8
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17 --id-file $choose_action.field_or_file.id_value
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6
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18 #end if
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19 --type $choose_action.choose_acs.input_type
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20
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21 #if $choose_action.choose_acs.input_type == 'assay':
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22 --operation $choose_action.choose_acs.operation_assay.operation_assay
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23 #if $choose_action.choose_acs.operation_assay.operation_assay == 'property':
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24 --property-value $choose_action.choose_acs.operation_assay.property_assay
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8
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25 #elif $choose_action.choose_acs.operation_assay.operation_assay == 'aids' or $choose_action.choose_acs.operation_assay.operation_assay == 'cids' or $choose_action.choose_acs.operation_assay.operation_assay == 'sids':
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26 --id-type $choose_action.choose_acs.operation_assay.ids_type_assay
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6
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27 #end if
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28 #elif $choose_action.choose_acs.input_type == 'compound':
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29 --operation $choose_action.choose_acs.operation_compound.operation_compound
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30 #if $choose_action.choose_acs.operation_compound.operation_compound == 'property':
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31 --property-value $choose_action.choose_acs.operation_compound.property_compound
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8
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32 #elif $choose_action.choose_acs.operation_compound.operation_compound == 'aids' or $choose_action.choose_acs.operation_compound.operation_compound == 'cids' or $choose_action.choose_acs.operation_compound.operation_compound == 'sids':
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33 --id-type $choose_action.choose_acs.operation_compound.ids_type_compound
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6
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34 #end if
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35 #else:
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36 --operation $choose_action.choose_acs.operation_substance.operation_substance
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37 #if $choose_action.choose_acs.operation_substance.operation_substance == 'property':
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38 --property-value $choose_action.choose_acs.operation_substance.property_substance
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8
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39 #elif $choose_action.choose_acs.operation_substance.operation_substance == 'aids' or $choose_action.choose_acs.operation_substance.operation_substance == 'cids' or $choose_action.choose_acs.operation_substance.operation_substance == 'sids':
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40 --id-type $choose_action.choose_acs.operation_substance.ids_type_substance
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6
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41 #end if
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42 #end if
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43 --outfile $output
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44 #elif $choose_action.action == 'compounds_for_assay':
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45 rest_tool_comp_for_assay.py
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8
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46 #if $choose_action.field_or_file.field_or_file_select == 'field':
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47 --aid $choose_action.field_or_file.id_value
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6
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48 #else:
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49 --aid-file $choose_action.field_or_file.id_value
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6
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50 #end if
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51 --outfile $output
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52 #elif $choose_action.action == 'assays_by_activity_or_target':
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53 rest_tool_assay_by_activity_or_target.py
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54 #if $choose_action.activity_or_target.activity_or_target == 'activity':
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55 --activity $choose_action.activity_or_target.activity
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56 #else:
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57 --target $choose_action.activity_or_target.target_id
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58 --target-type $choose_action.activity_or_target.target_identifier_type
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59 #end if
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60 --outfile $output
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8
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61 #elif $choose_action.action == 'advanced':
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62 rest_tool_advanced.py
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63 --outfile $output
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64 --type $choose_action.input_type.input_type_select
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65 --id-type $choose_action.input_type.namespace_id.namespace_id_select
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66 #if $choose_action.input_type.input_type_select == 'assay':
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67 #if $choose_action.input_type.namespace_id.namespace_id_select == 'aid':
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68 --id-type-ff $choose_action.input_type.namespace_id.field_or_file.field_or_file_select
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69 --id-value $choose_action.input_type.namespace_id.field_or_file.id_value
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70 #elif $choose_action.input_type.namespace_id.namespace_id_select == 'target':
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9
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71 --id-value $choose_action.input_type.namespace_id.target_select"/"$choose_action.input_type.namespace_id.target_value
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8
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72 #elif $choose_action.input_type.namespace_id.namespace_id_select == 'type':
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73 --id-value $choose_action.input_type.namespace_id.type_select
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74 #elif $choose_action.input_type.namespace_id.namespace_id_select == 'activity':
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75 --id-value $choose_action.input_type.namespace_id.activity_select
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76 #end if
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77
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78 --operation $choose_action.input_type.operation_assay.operation_assay_select
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79
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80 #if $choose_action.input_type.operation_assay.operation_assay_select == 'property':
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81 --operation-value $choose_action.input_type.operation_assay.operation_assay_select.property_assay
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82 #elif $choose_action.input_type.operation_assay.operation_assay_select == 'target':
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83 --operation-value $choose_action.input_type.operation_assay.operation_assay_select.target_assay
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9
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84 #elif $choose_action.input_type.operation_assay.operation_assay_select == 'xrefs':
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85 --operation-value $choose_action.input_type.operation_assay.xref_operation
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86 #elif $choose_action.input_type.operation_assay.operation_assay_select == 'doseresponse':
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87 --sid-filter $choose_action.input_type.operation_assay.doseresponse_sids
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8
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88 #elif $choose_action.input_type.operation_assay.operation_assay_select == 'aids' or $choose_action.input_type.operation_assay.operation_assay_select == 'cids' or $choose_action.input_type.operation_assay.operation_assay_select == 'sids':
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89 --ids-operation-type $choose_action.input_type.operation_assay.ids_type_assay
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90 #end if
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91 #elif $choose_action.input_type.input_type_select == 'compound':
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92 #if $choose_action.input_type.namespace_id.namespace_id_select == 'cid' or $choose_action.input_type.namespace_id.namespace_id_select == 'name' or $choose_action.input_type.namespace_id.namespace_id_select == 'smiles' or $choose_action.input_type.namespace_id.namespace_id_select == 'inchi' or $choose_action.input_type.namespace_id.namespace_id_select == 'inchikey' or $choose_action.input_type.namespace_id.namespace_id_select == 'sdf':
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93 --id-type-ff $choose_action.input_type.namespace_id.field_or_file.field_or_file_select
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94 --id-value $choose_action.input_type.namespace_id.field_or_file.id_value
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95 #elif $choose_action.input_type.namespace_id.namespace_id_select == 'xref':
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96 --xref $choose_action.input_type.namespace_id.xref_select
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97 --xref-value $choose_action.input_type.namespace_id.xref_value
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98 #end if
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99
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100 --operation $choose_action.input_type.operation_compound.operation_compound_select
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101 #if $choose_action.input_type.operation_compound.operation_compound_select == 'property':
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102 --operation-value $choose_action.input_type.operation_compound.property_compound
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103 #elif $choose_action.input_type.operation_compound.operation_compound_select == 'xrefs':
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9
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104 --operation-value $choose_action.input_type.operation_compound.xref_operation
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8
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105 #elif $choose_action.input_type.operation_compound.operation_compound_select == 'aids' or $choose_action.input_type.operation_compound.operation_compound_select == 'cids' or $choose_action.input_type.operation_compound.operation_compound_select == 'sids':
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106 --ids-operation-type $choose_action.input_type.operation_compound.ids_type_compound
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107 #end if
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108
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109 #elif $choose_action.input_type.input_type_select == 'substance':
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110 #if $choose_action.input_type.namespace_id.namespace_id_select == 'sid' or $choose_action.input_type.namespace_id.namespace_id_select == 'name':
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111 --id-type-ff $choose_action.input_type.namespace_id.field_or_file.field_or_file_select
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112 --id-value $choose_action.input_type.namespace_id.field_or_file.id_value
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113 #elif $choose_action.input_type.namespace_id.namespace_id_select == 'xrefs':
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114 --xref $choose_action.input_type.namespace_id.xref_select
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115 --xref-value $choose_action.input_type.namespace_id.xref_value
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116 #end if
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117 --operation $choose_action.input_type.operation_substance.operation_substance_select
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118 #if $choose_action.input_type.operation_substance.operation_substance_select == 'property':
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119 --operation-value $choose_action.input_type.operation_substance.operation_substance_select.property_substance
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120 #elif $choose_action.input_type.operation_substance.operation_substance_select == 'xref':
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9
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121 --operation-value $choose_action.input_type.operation_substance.xref_operation
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8
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122 #elif $choose_action.input_type.operation_substance.operation_substance_select == 'aids' or $choose_action.input_type.operation_substance.operation_substance_select == 'cids' or $choose_action.input_type.operation_substance.operation_substance_select == 'sids':
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123 --ids-operation-type $choose_action.input_type.operation_substance.ids_type_substance
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124 #end if
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125 #end if
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6
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126 #end if
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127 </command>
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128
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129 <inputs>
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130 <conditional name="choose_action">
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131 <param name="action" multiple="false" type="select" label="Choose action">
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132 <option value="specific_data">Get Data for specific Assay/Compound/Substance</option>
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133 <option value="compounds_for_assay">Get all compound IDs given BioAssay IDs</option>
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134 <option value="assays_by_activity_or_target">Get BioAssay IDs given activity/target</option>
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8
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135 <option value="advanced" selected="True">Advanced</option>
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6
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136 </param>
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137 <when value="search">
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138 <param name="input_type_search" multiple="false" type="select" label="Search for">
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8
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139 <expand macro="acs_options" />
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6
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140 </param>
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141 <param name="input_type" multiple="false" type="select" label="Search By">
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142 <option value="name">Name</option>
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143 </param>
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144 <param format="txt" name="search_name" type="text" label="Enter the Name" />
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145 </when>
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146 <when value="specific_data">
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8
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147 <expand macro="field_or_file" />
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6
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148 <conditional name="choose_acs">
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149 <param name="input_type" multiple="false" type="select" label="Input Type">
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8
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150 <expand macro="acs_options" />
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6
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151 </param>
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152
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153 <when value="assay">
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8
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154 <expand macro="conditional_operation_assay" />
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6
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155 </when>
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156 <when value="compound">
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8
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157 <expand macro="conditional_operation_compound" />
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6
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158 </when>
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159 <when value="substance">
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8
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160 <expand macro="conditional_operation_substance" />
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6
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161 </when>
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162 </conditional>
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163 </when>
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164 <!-- second option -->
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165 <when value="compounds_for_assay">
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8
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166 <expand macro="field_or_file" />
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6
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167 </when>
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168 <!-- third option -->
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169 <when value="assays_by_activity_or_target">
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170 <conditional name="activity_or_target">
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171 <param name="activity_or_target" multiple="false" type="select" label="Look for">
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172 <option value="target">Target</option>
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173 <option value="activity">Activity</option>
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174 </param>
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175 <when value="activity">
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176 <param format="txt" name="activity" type="text" label="Enter the activity" />
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177 </when>
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178
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179 <when value="target">
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180 <param name="target_identifier_type" multiple="false" type="select" label="Choose target identifier">
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181 <option value="gi">GI</option>
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182 <option value="geneid">Gene ID</option>
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183 <option value="genesymbol">Gene Symbol</option>
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184 </param>
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185 <param format="txt" name="target_id" type="text" label="Enter the target" />
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186 </when>
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187 </conditional>
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188 </when>
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8
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189 <when value="advanced">
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190 <expand macro="advanced2" />
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191 </when>
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6
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192 </conditional>
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193 </inputs>
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194 <outputs>
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9
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195 <data format="tabular" name="output">
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196 <change_format>
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197 <when input="choose_action.input_type.operation_assay.operation_assay_select" value="summary" format="xml" />
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198 <when input="choose_action.input_type.operation_assay.operation_assay_select" value="description" format="xml" />
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199 <when input="choose_action.input_type.operation_assay.operation_assay_select" value="classification" format="xml" />
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200 <when input="choose_action.input_type.operation_substance.operation_substance_select" value="summary" format="xml" />
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201 <when input="choose_action.input_type.operation_substance.operation_substance_select" value="description" format="xml" />
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202 <when input="choose_action.input_type.operation_substance.operation_substance_select" value="classification" format="xml" />
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203 <when input="choose_action.input_type.operation_compound.operation_compound_select" value="summary" format="xml" />
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204 <when input="choose_action.input_type.operation_compound.operation_compound_select" value="description" format="xml" />
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205 <when input="choose_action.input_type.operation_compound.operation_compound_select" value="classification" format="xml" />
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206 </change_format>
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207 </data>
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6
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208 </outputs>
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209 <tests>
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9
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210 <test>
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211 <output name="output">
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212 <assert_contents>
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213 <has_n_columns n="1" />
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214 <has_line_matching expression="[0-9]+" />
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215 </assert_contents>
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216 </output>
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217 <param name="choose_action.action" value="advanced" />
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218 <param name="choose_action.input_type.input_type_select" value="assay" />
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219 <param name="choose_action.input_type.namespace_id.namespace_id_select" value="target" />
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220 <param name="choose_action.input_type.namespace_id.target_select" value="genesymbol" />
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221 <param name="choose_action.input_type.namespace_id.target_value" value="usp2" />
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222 <param name="choose_action.input_type.operation_assay.operation_assay_select" value="aids" />
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223 </test>
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224 <test>
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225 <output name="output2">
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226 <assert_contents>
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227 <has_n_columns n="1" />
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228 <has_line_matching expression="[0-9]+" />
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229 </assert_contents>
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230 </output>
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231 <param name="choose_action.action" value="advanced" />
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232 <param name="choose_action.input_type.input_type_select" value="substance" />
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233 <param name="choose_action.input_type.namespace_id.namespace_id_select" value="xref" />
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234 <param name="choose_action.input_type.namespace_id.xref_select" value="PatentID" />
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235 <param name="choose_action.input_type.namespace_id.xref_value" value="EP0711162A1" />
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236 <param name="choose_action.input_type.operation_substance.operation_substance_select_select" value="cids" />
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237 </test>
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238 <!-- post test -->
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239 <test>
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240 <output name="output3">
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241 <assert_contents>
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242 <has_n_columns n="1" />
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243 <has_line_matching expression="[0-9]+" />
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244 </assert_contents>
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245 </output>
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246 <param name="choose_action.action" value="advanced" />
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247 <param name="choose_action.input_type.input_type_select" value="compound" />
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248 <param name="choose_action.input_type.namespace_id.namespace_id_select" value="inchi" />
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249 <param name="choose_action.input_type.namespace_id.field_or_file.field_or_file_select" value="file" />
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250 <param name="choose_action.input_type.namespace_id.field_or_file.id_value" value="postfile" />
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251 <param name="choose_action.input_type.operation_substance.operation_substance_select_select" value="cids" />
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252 </test>
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253 <test>
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254 <output name="output4">
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255 <assert_contents>
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256 <has_n_columns n="1" />
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257 <has_line_matching expression="[0-9]+" />
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258 </assert_contents>
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259 </output>
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260 <param name="choose_action.action" value="compounds_for_assay" />
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261 <param name="choose_action.input_type.input_type_select" value="compound" />
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262 <param name="choose_action.input_type.namespace_id.namespace_id_select" value="inchi" />
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263 <param name="choose_action.input_type.namespace_id.field_or_file.field_or_file_select" value="file" />
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264 <param name="choose_action.input_type.namespace_id.field_or_file.id_value" value="postfile" />
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265 <param name="choose_action.input_type.operation_substance.operation_substance_select_select" value="cids" />
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266 </test>
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6
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267 </tests>
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268 <help>
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269 **What it does**
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270
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8
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271 This tool fetches data from pubchem. The outputformat will be if possible csv > txt > xml
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6
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272 </help>
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273 </tool>
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