view rest_tool_macros.xml @ 10:a76d64d2ed44 draft default tip

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<macros>
    <xml name="aid_cid_sid">
        <option value="aids">AIDs</option>
        <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>
        <option value="component">component</option>
    </xml>
    <xml name="cid_cid_type_options">
        <option value="original">original</option>
        <option value="parent">parent</option>
        <option value="component">component</option>
        <option value="similar_2d">similar_2d</option>
        <option value="similar_3d">similar_3d</option>
        <option value="same_stereo">same_stereo</option>
        <option value="same_isotopes">same_isotopes</option>
        <option value="same_connectivity">same_connectivity</option>
        <option value="same_tautomer">same_tautomer</option>
        <option value="same_parent">same_parent</option>
        <option value="same_parent_stereo">same_parent_stereo</option>
        <option value="same_parent_isotopes">same_parent_isotopes</option>
        <option value="same_parent_connectivity">same_parent_connectivity</option>
        <option value="same_parent_tautomer">same_parent_tautomer</option>
    </xml>
    <xml name="sid_cid_type_options">
        <option value="all">all</option>
        <option value="standardized">standardized</option>
        <option value="component">component</option>
    </xml>
    <xml name="sid_sid_type_options">
        <option value="original">original</option>
        <option value="similar_2d">similar_2d</option>
        <option value="similar_3d">similar_3d</option>
        <option value="same_exact">same_exact</option>
        <option value="same_stereo">same_stereo</option>
        <option value="same_isotopes">same_isotopes</option>
        <option value="same_connectivity">same_connectivity</option>
        <option value="same_tautomer">same_tautomer</option>
        <option value="same_parent">same_parent</option>
        <option value="same_parent_stereo">same_parent_stereo</option>
        <option value="same_parent_isotopes">same_parent_isotopes</option>
        <option value="same_parent_connectivity">same_parent_connectivity</option>
        <option value="same_parent_tautomer">same_parent_tautomer</option>
    </xml>
    <xml name="aids_when_options">

                <option value="all" selected="True">all</option>
                <option value="active">active</option>
                <option value="inactive">inactive</option>
    </xml>
    <xml name="option_compound_substance">
        <option value="assaysummary">Assaysummary</option>
        <option value="synonyms">Synonyms</option>
        <option value="record">Record</option>
        <option value="classification">Classification</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_operation" 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="doseresponse">Doseresponse</option>
                                <option value="summary">Summary</option>
                                <option value="targets">Targets</option>
                            </param>
                            <when value="xrefs">
                                <param name="xref_operation" label="Choose Xrefs" multiple="true" type="select">
                                    <expand macro="xref_options" />
                                </param>
                            </when>
                            <when value="doseresponse">
                                <param name="doseresponse_sids" label="Filter by SIDs (comma separated)" 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_operation" 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>