diff rest_tool_macros.xml @ 8:3c1e862e8cd6 draft

Uploaded

--- a/rest_tool_macros.xml	Thu Apr 03 06:51:54 2014 -0400
+++ b/rest_tool_macros.xml	Fri May 02 05:40:28 2014 -0400
@@ -4,7 +4,11 @@
         <option value="cids">CIDs</option>
         <option value="sids">SIDs</option>
     </xml>
-    
+    <xml name="acs_options">
+        <option value="assay">BioAssay</option>
+        <option value="compound">Compound</option>
+        <option value="substance">Substance</option>
+    </xml>
     <xml name="cid_sid_type_options">
         <option value="all">all</option>
         <option value="standardized">standardized</option>
@@ -57,10 +61,191 @@
         <option value="synonyms">Synonyms</option>
         <option value="record">Record</option>
         <option value="classification">Classification</option>
-        <option value="property">Property</option>
         <option value="description">Discription</option>
+        <option value="xrefs">Xrefs</option>
+    </xml>
+    <xml name="compound_properties">
+    <param name="property_compound" type="select" multiple="true" label="Specify Property">
+        <option value="MolecularFormula">MolecularFormula</option>
+        <option value="MolecularWeight">MolecularWeight</option>
+        <option value="CanonicalSMILES">CanonicalSMILES</option>
+        <option value="IsomericSMILES">IsomericSMILES</option>
+        <option value="InChI">InChI</option>
+        <option value="InChIKey">InChIKey</option>
+        <option value="IUPACName">IUPACName</option>
+        <option value="XLogP">XLogP</option>
+        <option value="ExactMass">ExactMass</option>
+        <option value="MonoisotopicMass">MonoisotopicMass</option>
+        <option value="TPSA">TPSA</option>
+        <option value="Complexity">Complexity</option>
+        <option value="Charge">Charge</option>
+        <option value="HBondDonorCount">HBondDonorCount</option>
+        <option value="HBondAcceptorCount">HBondAcceptorCount</option>
+        <option value="RotatableBondCount">RotatableBondCount</option>
+        <option value="HeavyAtomCount">HeavyAtomCount</option>
+        <option value="IsotopeAtomCount">IsotopeAtomCount</option>
+        <option value="AtomStereoCount">AomStereoCount</option>
+        <option value="DefinedAtomStereoCount">DefinedAtomStereoCount</option>
+        <option value="UndefinedAtomStereoCount">UndefinedAtomStereoCount</option>
+        <option value="BondStereoCount">BondStereoCount</option>
+        <option value="DefinedBondStereoCount">DefinedBondStereoCount</option>
+        <option value="UndefinedBondStereoCount">UndefinedBondStereoCount</option>
+        <option value="CovalentUnitCount">CovalentUnitCount</option>
+        <option value="Volume3D">lume3D</option>
+        <option value="XStericQuadrupole3D">XStericQuadrupole3D</option>
+        <option value="YStericQuadrupole3D">YStericQuadrupole3D</option>
+        <option value="ZStericQuadrupole3D">ZStericQuadrupole3D</option>
+        <option value="FeatureCount3D">FeatureCount3D</option>
+        <option value="FeatureAcceptorCount3D">FeatureAcceptorCount3D</option>
+        <option value="FeatureDonorCount3D">FeatureDonorCount3D</option>
+        <option value="FeatureAnionCount3D">FeatureAnionCount3D</option>
+        <option value="FeatureCationCount3D">FeatureCationCount3D</option>
+        <option value="FeatureRingCount3D">FeatureRingCount3D</option>
+        <option value="FeatureHydrophobeCount3D">FeatureHydrophobeCount3D</option>
+        <option value="ConformerModelRMSD3D">ConformerModelRMSD3D</option>
+        <option value="EffectiveRotorCount3D">EffectiveRotorCount3D</option>
+        <option value="ConformerCount3D">ConformerCount3D</option>
+    </param>
+    </xml>
+    <xml name="xref_select">
+        <param name="xref_compound_select" label="Choose Xrefs" multiple="true" type="select">
+            <expand macro="xref_options" />
+        </param>
+    </xml>
+
+    <xml name="xref_options">
+        <option value="RegistryID">external registry identifier</option>
+        <option value="RN">registry number</option>
+        <option value="PubMedID">NCBI PubMed identifier</option>
+        <option value="MMDBID">NCBI MMDB identifier</option>
+        <option value="DBURL">external database home page URL</option>
+        <option value="SBURL">external database substance URL</option>
+        <option value="ProteinGI">NCBI protein GI</option>
+        <option value="NucleotideGI">NCBI nucleotide GI</option>
+        <option value="TaxonomyID">NCBI taxonomy identifier</option>
+        <option value="MIMID NCBI">MIM identifier</option>
+        <option value="GeneID NCBI">gene identifier</option>
+        <option value="ProbeID NCBI">probe identifier</option>
+        <option value="PatentID">patent identifier</option>
+        <option value="SourceName">external depositor name</option>
+        <option value="SourceCategory">depositor category(ies)</option>
+    </xml>
+    <xml name="field_or_file">
+        <conditional name="field_or_file">
+            <param name="field_or_file_select" multiple="false" type="select" label="Specify Identifiers by">
+                <option value="field">Textfield</option>
+                <option value="file">File</option>
+            </param>
+            <when value="field">
+                <param format="txt" name="id_value" type="text" area="true" size="10x40" label="Enter the Identifiers (one per line)" />
+            </when>
+            <when value="file">
+                <param format="txt,csv" name="id_value" type="data" label="Select file" />
+            </when>
+        </conditional>
     </xml>
-    
+    <xml name="conditional_operation_compound">
+        <conditional name="operation_compound">
+                            <param name="operation_compound_select" type="select" multiple="false" label="Operation">
+                                <expand macro="aid_cid_sid" />
+                                <expand macro="option_compound_substance" />
+                                <option value="property">Property</option>
+                            </param>
+                            <when value="property">
+                                <expand macro="compound_properties" />
+                            </when>
+                            <when value="xrefs">
+                                <param name="xref_compound" label="Choose Xrefs" multiple="true" type="select">
+                                    <expand macro="xref_options" />
+                                </param>
+                            </when>
+                            <when value="aids">
+                                <param name="ids_type_compound" multiple="false" type="select" label="AID Type">
+                                    <expand macro="aids_when_options" />
+                                </param>
+                            </when>
+                            <when value="sids">
+                                <param name="ids_type_compound" multiple="false" type="select" label="SID Type">
+                                    <expand macro="cid_sid_type_options" />
+                                </param>
+                            </when>
+                            <when value="cids">
+                                <param name="ids_type_compound" multiple="false" type="select" label="CID Type">
+                                    <expand macro="cid_cid_type_options" />
+                                </param>
+                            </when>
+        </conditional>
+    </xml>
+    <xml name="conditional_operation_assay">
+    <conditional name="operation_assay">
+                            <param name="operation_assay_select" type="select" multiple="false" label="Operation">
+                                <expand macro="aid_cid_sid" />
+                                <option value="record">Record</option>
+                                <option value="classification">Classification</option>
+                                <option value="xrefs">Xrefs</option>
+                                <option value="description">Discription</option>
+                                <option value="summary">Summary</option>
+                                <option value="targets">Targets</option>
+                            </param>
+                            <when value="xrefs">
+                                <param name="property_assay" label="Specify Property" type="text" />
+                            </when>
 
- 
+                            <when value="targets">
+                                <param name="target_assay" label="Specify Target" type="select" multiple="true">
+                                    <option value="ProteinGI">NCBI GI of a protein sequence</option>
+                                    <option value="ProteinName">Protein Name</option>
+                                    <option value="GeneID">NCBI Gene database identifier</option>
+                                    <option value="GeneSymbol">Gene Symbol</option>
+                                </param>
+                            </when>
+                            <when value="aids">
+                                <param name="ids_type_assay" multiple="false" type="select" label="AID Type">
+                                    <expand macro="aids_when_options" />
+                                </param>
+                            </when>
+                            <when value="cids">
+                                <param name="ids_type_assay" multiple="false" type="select" label="CID Type">
+                                    <expand macro="aids_when_options" />
+                                    
+                                </param>
+                            </when>
+                            <when value="sids">
+                                <param name="ids_type_assay" multiple="false" type="select" label="SID Type">
+                                    <expand macro="aids_when_options" />
+                                    <option value="doseresponse">doseresponse</option>
+                                </param>
+                            </when>
+                        </conditional>
+    </xml>
+    <xml name="conditional_operation_substance">
+    <conditional name="operation_substance">
+                            <param name="operation_substance_select" type="select" multiple="false" label="Operation">
+                                <expand macro="aid_cid_sid" />
+                                <expand macro="option_compound_substance" />
+                            </param>
+
+                            <when value="xrefs">
+                                <param name="xref_substance" label="Choose Xrefs" multiple="true" type="select">
+                                    <expand macro="xref_options" />
+                                </param>
+                            </when>
+                            <when value="aids">
+                                <param name="ids_type_substance" multiple="false" type="select" label="AID Type">
+                                    <expand macro="aids_when_options" />
+                                </param>
+                            </when>
+                            <when value="cids">
+                                <param name="ids_type_substance" multiple="false" type="select" label="CID Type">
+                                    <expand macro="sid_cid_type_options" />
+                                </param>
+                            </when>
+                            <when value="sids">
+                                <param name="ids_type_substance" multiple="false" type="select" label="SID Type">
+                                    <expand macro="sid_sid_type_options" />
+                                </param>
+                            </when>
+                            
+                        </conditional>
+    </xml>
 </macros>