Mercurial > repos > iuc > ebi_search_rest_results
diff macros.xml @ 3:42d5e40fcd0b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 31d1c92a4c12b6a78693dc5091a08536a075285e
| author | iuc |
|---|---|
| date | Thu, 09 Feb 2017 12:02:58 -0500 |
| parents | b6029f2c71cb |
| children |
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--- a/macros.xml Sat Jan 21 14:41:05 2017 -0500 +++ b/macros.xml Thu Feb 09 12:02:58 2017 -0500 @@ -53,6 +53,7 @@ <option value="imgt-hla">IMGT/HLA</option> <option value="ipd-kir">IPD-KIR</option> <option value="ipd-mhc">IPD-MHC</option> + <option value="identifiers_registry">Identifiers.org registry</option> <option value="intact-complexes">IntAct Complexes</option> <option value="intact-experiments">IntAct Experiments</option> <option value="intact-interactions">IntAct Interactions</option> @@ -495,7 +496,6 @@ <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract"> <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> <option value="DOI" selected="true">DOI</option> - <option value="EC" selected="true">EC</option> <option value="EMBLCDS" selected="true">EMBLCDS</option> <option value="ENA" selected="true">ENA</option> <option value="ENA-CON" selected="true">ENA-CON</option> @@ -524,7 +524,6 @@ <param name="query_field" type="select" label="Fields"> <option value="BIOSAMPLE">BIOSAMPLE</option> <option value="DOI">DOI</option> - <option value="EC">EC</option> <option value="EMBLCDS">EMBLCDS</option> <option value="EMBLCDS_version">EMBLCDS_version</option> <option value="ENA">ENA</option> @@ -547,7 +546,6 @@ <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> <option value="WORMBASE">WORMBASE</option> <option value="acc">acc</option> - <option value="bio_material">bio_material</option> <option value="creation_date">creation_date</option> <option value="culture_collection">culture_collection</option> <option value="data_class">data_class</option> @@ -1751,7 +1749,6 @@ <option value="UNIPROT">UNIPROT</option> <option value="age">age</option> <option value="biopsy_site">biopsy_site</option> - <option value="biotic_plant_treatment">biotic_plant_treatment</option> <option value="block">block</option> <option value="cell_cycle_stage">cell_cycle_stage</option> <option value="cell_line">cell_line</option> @@ -3952,6 +3949,73 @@ </repeat> </when> + <when value="identifiers_registry"> + <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract"> + <option value="COLLECTION" selected="true">COLLECTION</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="institution" selected="true">institution</option> + <option value="location" selected="true">location</option> + <option value="name" selected="true">name</option> + <option value="obsolete" selected="true">obsolete</option> + <option value="official" selected="true">official</option> + <option value="pattern" selected="true">pattern</option> + <option value="tag" selected="true">tag</option> + <option value="type" selected="true">type</option> + <option value="uptime" selected="true">uptime</option> + <option value="uptime-range" selected="true">uptime-range</option> + <option value="uri" selected="true">uri</option> + </param> + <repeat name="queries" title="Add a query"> + <param name="combination_operation" type="select" label="Combination operation"> + <option value="AND">AND</option> + <option value="OR">OR</option> + <option value="NOT">NOT</option> + </param> + <param name="query_field" type="select" label="Fields"> + <option value="COLLECTION">COLLECTION</option> + <option value="DOI">DOI</option> + <option value="PUBMED">PUBMED</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="institution">institution</option> + <option value="location">location</option> + <option value="name">name</option> + <option value="namespace">namespace</option> + <option value="obsolete">obsolete</option> + <option value="official">official</option> + <option value="pattern">pattern</option> + <option value="provider_code">provider_code</option> + <option value="tag">tag</option> + <option value="type">type</option> + <option value="uptime">uptime</option> + <option value="uptime-range">uptime-range</option> + <option value="uri">uri</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation"> + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + <when value="intact-complexes"> <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract"> <option value="CHEMBL" selected="true">CHEMBL</option> @@ -3968,7 +4032,6 @@ <option value="INTERPRO" selected="true">INTERPRO</option> <option value="MATRIXDB" selected="true">MATRIXDB</option> <option value="MINT" selected="true">MINT</option> - <option value="OMIM" selected="true">OMIM</option> <option value="ORPHANET" selected="true">ORPHANET</option> <option value="PDBE" selected="true">PDBE</option> <option value="PROTEIN_ONTOLOGY" selected="true">PROTEIN_ONTOLOGY</option> @@ -4003,7 +4066,6 @@ <option value="INTERPRO">INTERPRO</option> <option value="MATRIXDB">MATRIXDB</option> <option value="MINT">MINT</option> - <option value="OMIM">OMIM</option> <option value="ORPHANET">ORPHANET</option> <option value="PDBE">PDBE</option> <option value="PROTEIN_ONTOLOGY">PROTEIN_ONTOLOGY</option> @@ -5374,7 +5436,6 @@ <option value="KEGG" selected="true">KEGG</option> <option value="METABOLIGHTS" selected="true">METABOLIGHTS</option> <option value="MTBLS" selected="true">MTBLS</option> - <option value="PUBCHEM" selected="true">PUBCHEM</option> <option value="PUBMED" selected="true">PUBMED</option> <option value="dataset_file" selected="true">dataset_file</option> <option value="description" selected="true">description</option> @@ -5409,7 +5470,6 @@ <option value="KEGG">KEGG</option> <option value="METABOLIGHTS">METABOLIGHTS</option> <option value="MTBLS">MTBLS</option> - <option value="PUBCHEM">PUBCHEM</option> <option value="PUBMED">PUBMED</option> <option value="apodisation_zero_filling_and_fourier_transformation_protocol">apodisation_zero_filling_and_fourier_transformation_protocol</option> <option value="author">author</option> @@ -5417,14 +5477,12 @@ <option value="batch_correction_protocol">batch_correction_protocol</option> <option value="chromatography_protocol">chromatography_protocol</option> <option value="data_analysis_protocol">data_analysis_protocol</option> - <option value="data_normalization_protocol">data_normalization_protocol</option> <option value="data_transformation_protocol">data_transformation_protocol</option> <option value="description">description</option> <option value="domain_source">domain_source</option> <option value="extraction_protocol">extraction_protocol</option> <option value="formula">formula</option> <option value="full_dataset_link">full_dataset_link</option> - <option value="gc_ms_protocol">gc_ms_protocol</option> <option value="glog_transformation_protocol">glog_transformation_protocol</option> <option value="growth_conditions_protocol">growth_conditions_protocol</option> <option value="histology_protocol">histology_protocol</option> @@ -5432,8 +5490,6 @@ <option value="inchi">inchi</option> <option value="instrument_platform">instrument_platform</option> <option value="iupac">iupac</option> - <option value="labeling_protocol">labeling_protocol</option> - <option value="lc_ms_protocol">lc_ms_protocol</option> <option value="mass_calibration_and_sim_stitching_protocol">mass_calibration_and_sim_stitching_protocol</option> <option value="mass_spec_protocol">mass_spec_protocol</option> <option value="metabolite_id_protocol">metabolite_id_protocol</option> @@ -5448,12 +5504,14 @@ <option value="organism_part">organism_part</option> <option value="pqn_normalisation_protocol">pqn_normalisation_protocol</option> <option value="preparation_protocol">preparation_protocol</option> + <option value="preprocessing_protocol">preprocessing_protocol</option> <option value="publication">publication</option> <option value="publication_date">publication_date</option> <option value="replicate_filtering_protocol">replicate_filtering_protocol</option> <option value="repository">repository</option> <option value="sample_collection_protocol">sample_collection_protocol</option> <option value="sample_filtering_including_tic_filtering_blank_filtering_and_missing_value_filtering_protocol">sample_filtering_including_tic_filtering_blank_filtering_and_missing_value_filtering_protocol</option> + <option value="sample_preparation_protocol">sample_preparation_protocol</option> <option value="software_processing_protocol">software_processing_protocol</option> <option value="spectral_cleaning_protocol">spectral_cleaning_protocol</option> <option value="study">study</option> @@ -5811,7 +5869,7 @@ <when value="hmmer_seq"> <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract"> <option value="ENSEMBL" selected="true">ENSEMBL</option> - <option value="PDB" selected="true">PDB</option> + <option value="PDBE" selected="true">PDBE</option> <option value="UNIPROT" selected="true">UNIPROT</option> <option value="content" selected="true">content</option> <option value="domain_source" selected="true">domain_source</option> @@ -5825,7 +5883,7 @@ </param> <param name="query_field" type="select" label="Fields"> <option value="ENSEMBL">ENSEMBL</option> - <option value="PDB">PDB</option> + <option value="PDBE">PDBE</option> <option value="UNIPROT">UNIPROT</option> <option value="domain_source">domain_source</option> <option value="id">id</option> @@ -6346,7 +6404,6 @@ <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> <option value="DOI" selected="true">DOI</option> <option value="EMBL" selected="true">EMBL</option> - <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> <option value="PUBMED" selected="true">PUBMED</option> <option value="SILVA-LSU" selected="true">SILVA-LSU</option> <option value="SILVA-SSU" selected="true">SILVA-SSU</option> @@ -6368,7 +6425,6 @@ <option value="DOI">DOI</option> <option value="EMBL">EMBL</option> <option value="MD5">MD5</option> - <option value="PATENT_NUMBER">PATENT_NUMBER</option> <option value="PROJECT">PROJECT</option> <option value="PUBMED">PUBMED</option> <option value="SILVA-LSU">SILVA-LSU</option> @@ -7092,6 +7148,7 @@ <option value="GO" selected="true">GO</option> <option value="GREENGENES" selected="true">GREENGENES</option> <option value="GTRNADB" selected="true">GTRNADB</option> + <option value="HGNC" selected="true">HGNC</option> <option value="LNCIPEDIA" selected="true">LNCIPEDIA</option> <option value="LNCRNADB" selected="true">LNCRNADB</option> <option value="MIRBASE" selected="true">MIRBASE</option> @@ -7147,6 +7204,7 @@ <option value="GO">GO</option> <option value="GREENGENES">GREENGENES</option> <option value="GTRNADB">GTRNADB</option> + <option value="HGNC">HGNC</option> <option value="LNCIPEDIA">LNCIPEDIA</option> <option value="LNCRNADB">LNCRNADB</option> <option value="MIRBASE">MIRBASE</option> @@ -7221,7 +7279,6 @@ <when value="reactome"> <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract"> <option value="ARACYC" selected="true">ARACYC</option> - <option value="BIOMODELS_DATABASE" selected="true">BIOMODELS_DATABASE</option> <option value="CAS" selected="true">CAS</option> <option value="CHEBI" selected="true">CHEBI</option> <option value="COMPOUND" selected="true">COMPOUND</option> @@ -7232,12 +7289,12 @@ <option value="EMBL" selected="true">EMBL</option> <option value="ENSEMBL" selected="true">ENSEMBL</option> <option value="GENECARDS" selected="true">GENECARDS</option> + <option value="GLYCAN" selected="true">GLYCAN</option> <option value="GO" selected="true">GO</option> <option value="HMDB_METABOLITE" selected="true">HMDB_METABOLITE</option> <option value="HMDB_PROTEIN" selected="true">HMDB_PROTEIN</option> <option value="INTACT" selected="true">INTACT</option> <option value="KEGG_GENE" selected="true">KEGG_GENE</option> - <option value="KEGG_GLYCAN" selected="true">KEGG_GLYCAN</option> <option value="KNAPSACK" selected="true">KNAPSACK</option> <option value="MIRBASE" selected="true">MIRBASE</option> <option value="NCBI_NUCLEOTIDE" selected="true">NCBI_NUCLEOTIDE</option> @@ -7278,7 +7335,6 @@ </param> <param name="query_field" type="select" label="Fields"> <option value="ARACYC">ARACYC</option> - <option value="BIOMODELS_DATABASE">BIOMODELS_DATABASE</option> <option value="CAS">CAS</option> <option value="CHEBI">CHEBI</option> <option value="COMPOUND">COMPOUND</option> @@ -7289,12 +7345,12 @@ <option value="EMBL">EMBL</option> <option value="ENSEMBL">ENSEMBL</option> <option value="GENECARDS">GENECARDS</option> + <option value="GLYCAN">GLYCAN</option> <option value="GO">GO</option> <option value="HMDB_METABOLITE">HMDB_METABOLITE</option> <option value="HMDB_PROTEIN">HMDB_PROTEIN</option> <option value="INTACT">INTACT</option> <option value="KEGG_GENE">KEGG_GENE</option> - <option value="KEGG_GLYCAN">KEGG_GLYCAN</option> <option value="KNAPSACK">KNAPSACK</option> <option value="MIRBASE">MIRBASE</option> <option value="NCBI_NUCLEOTIDE">NCBI_NUCLEOTIDE</option> @@ -7474,7 +7530,11 @@ <when value="ebiweb_resources"> <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract"> + <option value="activity" selected="true">activity</option> + <option value="category" selected="true">category</option> + <option value="cluster" selected="true">cluster</option> <option value="description" selected="true">description</option> + <option value="domain" selected="true">domain</option> <option value="domain_source" selected="true">domain_source</option> <option value="id" selected="true">id</option> <option value="logo" selected="true">logo</option> @@ -7871,6 +7931,7 @@ <option value="AGRICOLA" selected="true">AGRICOLA</option> <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> <option value="CABRI" selected="true">CABRI</option> + <option value="CCAP" selected="true">CCAP</option> <option value="COMPARE-REFGENOME" selected="true">COMPARE-REFGENOME</option> <option value="DOI" selected="true">DOI</option> <option value="EC" selected="true">EC</option> @@ -7888,6 +7949,7 @@ <option value="HGNC" selected="true">HGNC</option> <option value="INTERPRO" selected="true">INTERPRO</option> <option value="IPD-MHC" selected="true">IPD-MHC</option> + <option value="ISHAM-ITS" selected="true">ISHAM-ITS</option> <option value="MGI" selected="true">MGI</option> <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> <option value="PDB" selected="true">PDB</option> @@ -7902,6 +7964,7 @@ <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> <option value="UNITE" selected="true">UNITE</option> + <option value="VBASE2" selected="true">VBASE2</option> <option value="ZFIN" selected="true">ZFIN</option> <option value="acc" selected="true">acc</option> <option value="description" selected="true">description</option> @@ -7918,6 +7981,7 @@ <option value="AGRICOLA">AGRICOLA</option> <option value="BIOSAMPLE">BIOSAMPLE</option> <option value="CABRI">CABRI</option> + <option value="CCAP">CCAP</option> <option value="COMPARE-REFGENOME">COMPARE-REFGENOME</option> <option value="DOI">DOI</option> <option value="EC">EC</option> @@ -7941,6 +8005,7 @@ <option value="IMGT_LIGM">IMGT_LIGM</option> <option value="INTERPRO">INTERPRO</option> <option value="IPD-MHC">IPD-MHC</option> + <option value="ISHAM-ITS">ISHAM-ITS</option> <option value="MD5">MD5</option> <option value="MGI">MGI</option> <option value="PATENT_NUMBER">PATENT_NUMBER</option> @@ -7959,6 +8024,7 @@ <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> <option value="UNITE">UNITE</option> + <option value="VBASE2">VBASE2</option> <option value="ZFIN">ZFIN</option> <option value="acc">acc</option> <option value="bio_material">bio_material</option> @@ -8696,6 +8762,7 @@ <option value="REPRODUCTION-2DPAGE" selected="true">REPRODUCTION-2DPAGE</option> <option value="RGD" selected="true">RGD</option> <option value="SABIO-RK" selected="true">SABIO-RK</option> + <option value="SFLD" selected="true">SFLD</option> <option value="SGD" selected="true">SGD</option> <option value="SIGNALINK" selected="true">SIGNALINK</option> <option value="SIGNOR" selected="true">SIGNOR</option> @@ -8879,6 +8946,7 @@ <option value="SAAS">SAAS</option> <option value="SABIO-RK">SABIO-RK</option> <option value="SAM">SAM</option> + <option value="SFLD">SFLD</option> <option value="SGD">SGD</option> <option value="SIGNALINK">SIGNALINK</option> <option value="SIGNOR">SIGNOR</option> @@ -9147,21 +9215,19 @@ <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> <option value="PDB" selected="true">PDB</option> <option value="PROTEIN_ID" selected="true">PROTEIN_ID</option> - <option value="REACTOME" selected="true">REACTOME</option> <option value="REFSEQ_MRNA" selected="true">REFSEQ_MRNA</option> <option value="REFSEQ_MRNA_PREDICTED" selected="true">REFSEQ_MRNA_PREDICTED</option> <option value="REFSEQ_NCRNA" selected="true">REFSEQ_NCRNA</option> <option value="REFSEQ_PEPTIDE" selected="true">REFSEQ_PEPTIDE</option> <option value="REFSEQ_PEPTIDE_PREDICTED" selected="true">REFSEQ_PEPTIDE_PREDICTED</option> - <option value="SCHISTODB" selected="true">SCHISTODB</option> <option value="UNIGENE" selected="true">UNIGENE</option> <option value="UNIPARC" selected="true">UNIPARC</option> - <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option> <option value="UNIPROT" selected="true">UNIPROT</option> <option value="WIKIGENE" selected="true">WIKIGENE</option> <option value="WORMBASE_GENE" selected="true">WORMBASE_GENE</option> <option value="WORMBASE_GSEQNAME" selected="true">WORMBASE_GSEQNAME</option> <option value="WORMBASE_LOCUS" selected="true">WORMBASE_LOCUS</option> + <option value="WORMBASE_ORTHOLOG" selected="true">WORMBASE_ORTHOLOG</option> <option value="WORMBASE_TRANSCRIPT" selected="true">WORMBASE_TRANSCRIPT</option> <option value="WORMPEP_ID" selected="true">WORMPEP_ID</option> <option value="description" selected="true">description</option> @@ -9204,21 +9270,19 @@ <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> <option value="PDB">PDB</option> <option value="PROTEIN_ID">PROTEIN_ID</option> - <option value="REACTOME">REACTOME</option> <option value="REFSEQ_MRNA">REFSEQ_MRNA</option> <option value="REFSEQ_MRNA_PREDICTED">REFSEQ_MRNA_PREDICTED</option> <option value="REFSEQ_NCRNA">REFSEQ_NCRNA</option> <option value="REFSEQ_PEPTIDE">REFSEQ_PEPTIDE</option> <option value="REFSEQ_PEPTIDE_PREDICTED">REFSEQ_PEPTIDE_PREDICTED</option> - <option value="SCHISTODB">SCHISTODB</option> <option value="UNIGENE">UNIGENE</option> <option value="UNIPARC">UNIPARC</option> - <option value="UNIPATHWAY">UNIPATHWAY</option> <option value="UNIPROT">UNIPROT</option> <option value="WIKIGENE">WIKIGENE</option> <option value="WORMBASE_GENE">WORMBASE_GENE</option> <option value="WORMBASE_GSEQNAME">WORMBASE_GSEQNAME</option> <option value="WORMBASE_LOCUS">WORMBASE_LOCUS</option> + <option value="WORMBASE_ORTHOLOG">WORMBASE_ORTHOLOG</option> <option value="WORMBASE_TRANSCRIPT">WORMBASE_TRANSCRIPT</option> <option value="WORMPEP_ID">WORMPEP_ID</option> <option value="collection">collection</option>