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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
| author | bgruening |
|---|---|
| date | Tue, 06 Aug 2024 14:49:45 +0000 |
| parents | 468c71dac78a |
| children |
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<tool id="uniprot" name="UniProt" version="0.6" profile="23.1"> <description>ID mapping and retrieval</description> <requirements> <requirement type="package" version="2.25.1">requests</requirement> </requirements> <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> <command detect_errors="aggressive"><![CDATA[ cut -f ${id_column} '$infile' > id_file.tabular && python '$__tool_directory__/uniprot.py' #if $tool.tool_choice == "retrieve": retrieve -f $tool.format id_file.tabular ./output #elif $tool.tool_choice == "map": map --format tsv "$from_cond.from" "$from_cond.to" id_file.tabular ./output #end if ]]></command> <inputs> <param name="infile" type="data" format="tabular" label="Input file with IDs" help="One ID in each line."/> <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/> <conditional name="tool"> <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help=""> <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option> <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option> </param> <when value="map"> <!-- conditional auto generated with python tools/uniprot_rest_interface/uniprot.py menu --> <conditional name="from_cond"> <param name="from" type="select" label="Source database:"> <option value="UniProtKB_AC-ID">UniProt - UniProtKB AC/ID</option> <option value="UniParc">UniProt - UniParc</option> <option value="UniRef50">UniProt - UniRef50</option> <option value="UniRef90">UniProt - UniRef90</option> <option value="UniRef100">UniProt - UniRef100</option> <option value="Gene_Name">UniProt - Gene Name</option> <option value="CRC64">UniProt - CRC64</option> <option value="CCDS">Sequence DBs - CCDS</option> <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option> <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option> <option value="GI_number">Sequence DBs - GI number</option> <option value="PIR">Sequence DBs - PIR</option> <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option> <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option> <option value="PDB">3D structure DBs - PDB</option> <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option> <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option> <option value="DIP">Protein-protein interaction DBs - DIP</option> <option value="STRING">Protein-protein interaction DBs - STRING</option> <option value="ChEMBL">Chemistry - ChEMBL</option> <option value="DrugBank">Chemistry - DrugBank</option> <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option> <option value="SwissLipids">Chemistry - SwissLipids</option> <option value="Allergome">Protein family/group DBs - Allergome</option> <option value="CLAE">Protein family/group DBs - CLAE</option> <option value="ESTHER">Protein family/group DBs - ESTHER</option> <option value="MEROPS">Protein family/group DBs - MEROPS</option> <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option> <option value="REBASE">Protein family/group DBs - REBASE</option> <option value="TCDB">Protein family/group DBs - TCDB</option> <option value="GlyConnect">PTM DBs - GlyConnect</option> <option value="BioMuta">Genetic variation DBs - BioMuta</option> <option value="DMDM">Genetic variation DBs - DMDM</option> <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option> <option value="CPTAC">Proteomic DBs - CPTAC</option> <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option> <option value="DNASU">Protocols and materials DBs - DNASU</option> <option value="Ensembl">Genome annotation DBs - Ensembl</option> <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option> <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option> <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option> <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option> <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option> <option value="GeneID">Genome annotation DBs - GeneID</option> <option value="KEGG">Genome annotation DBs - KEGG</option> <option value="PATRIC">Genome annotation DBs - PATRIC</option> <option value="UCSC">Genome annotation DBs - UCSC</option> <option value="WBParaSite">Genome annotation DBs - WBParaSite</option> <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option> <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option> <option value="Araport">Organism-specific DBs - Araport</option> <option value="CGD">Organism-specific DBs - CGD</option> <option value="ConoServer">Organism-specific DBs - ConoServer</option> <option value="dictyBase">Organism-specific DBs - dictyBase</option> <option value="EchoBASE">Organism-specific DBs - EchoBASE</option> <option value="euHCVdb">Organism-specific DBs - euHCVdb</option> <option value="FlyBase">Organism-specific DBs - FlyBase</option> <option value="GeneCards">Organism-specific DBs - GeneCards</option> <option value="GeneReviews">Organism-specific DBs - GeneReviews</option> <option value="HGNC">Organism-specific DBs - HGNC</option> <option value="LegioList">Organism-specific DBs - LegioList</option> <option value="Leproma">Organism-specific DBs - Leproma</option> <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option> <option value="MGI">Organism-specific DBs - MGI</option> <option value="MIM">Organism-specific DBs - MIM</option> <option value="neXtProt">Organism-specific DBs - neXtProt</option> <option value="OpenTargets">Organism-specific DBs - OpenTargets</option> <option value="Orphanet">Organism-specific DBs - Orphanet</option> <option value="PharmGKB">Organism-specific DBs - PharmGKB</option> <option value="PomBase">Organism-specific DBs - PomBase</option> <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option> <option value="RGD">Organism-specific DBs - RGD</option> <option value="SGD">Organism-specific DBs - SGD</option> <option value="TubercuList">Organism-specific DBs - TubercuList</option> <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option> <option value="VGNC">Organism-specific DBs - VGNC</option> <option value="WormBase">Organism-specific DBs - WormBase</option> <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option> <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option> <option value="Xenbase">Organism-specific DBs - Xenbase</option> <option value="ZFIN">Organism-specific DBs - ZFIN</option> <option value="eggNOG">Phylogenomic DBs - eggNOG</option> <option value="GeneTree">Phylogenomic DBs - GeneTree</option> <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option> <option value="OMA">Phylogenomic DBs - OMA</option> <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option> <option value="TreeFam">Phylogenomic DBs - TreeFam</option> <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option> <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option> <option value="Reactome">Enzyme and pathway DBs - Reactome</option> <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option> <option value="ChiTaRS">Miscellaneous - ChiTaRS</option> <option value="GeneWiki">Miscellaneous - GeneWiki</option> <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option> <option value="PHI-base">Miscellaneous - PHI-base</option> <option value="CollecTF">Gene expression DBs - CollecTF</option> <option value="DisProt">Family and domain DBs - DisProt</option> <option value="IDEAL">Family and domain DBs - IDEAL</option> </param> <when value="UniProtKB_AC-ID"> <param name="to" type="select" label="Target database:"> <option value="CCDS">Sequence DBs - CCDS</option> <option value="PIR">Sequence DBs - PIR</option> <option value="PDB">3D structure DBs - PDB</option> <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option> <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option> <option value="DIP">Protein-protein interaction DBs - DIP</option> <option value="STRING">Protein-protein interaction DBs - STRING</option> <option value="ChEMBL">Chemistry - ChEMBL</option> <option value="DrugBank">Chemistry - DrugBank</option> <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option> <option value="SwissLipids">Chemistry - SwissLipids</option> <option value="Allergome">Protein family/group DBs - Allergome</option> <option value="ESTHER">Protein family/group DBs - ESTHER</option> <option value="MEROPS">Protein family/group DBs - MEROPS</option> <option value="CLAE">Protein family/group DBs - CLAE</option> <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option> <option value="REBASE">Protein family/group DBs - REBASE</option> <option value="TCDB">Protein family/group DBs - TCDB</option> <option value="GlyConnect">PTM DBs - GlyConnect</option> <option value="BioMuta">Genetic variation DBs - BioMuta</option> <option value="DMDM">Genetic variation DBs - DMDM</option> <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option> <option value="CPTAC">Proteomic DBs - CPTAC</option> <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option> <option value="DNASU">Protocols and materials DBs - DNASU</option> <option value="Ensembl">Genome annotation DBs - Ensembl</option> <option value="GeneID">Genome annotation DBs - GeneID</option> <option value="KEGG">Genome annotation DBs - KEGG</option> <option value="PATRIC">Genome annotation DBs - PATRIC</option> <option value="UCSC">Genome annotation DBs - UCSC</option> <option value="WBParaSite">Genome annotation DBs - WBParaSite</option> <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option> <option value="Araport">Organism-specific DBs - Araport</option> <option value="CGD">Organism-specific DBs - CGD</option> <option value="ConoServer">Organism-specific DBs - ConoServer</option> <option value="dictyBase">Organism-specific DBs - dictyBase</option> <option value="EchoBASE">Organism-specific DBs - EchoBASE</option> <option value="euHCVdb">Organism-specific DBs - euHCVdb</option> <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option> <option value="FlyBase">Organism-specific DBs - FlyBase</option> <option value="GeneCards">Organism-specific DBs - GeneCards</option> <option value="GeneReviews">Organism-specific DBs - GeneReviews</option> <option value="HGNC">Organism-specific DBs - HGNC</option> <option value="LegioList">Organism-specific DBs - LegioList</option> <option value="Leproma">Organism-specific DBs - Leproma</option> <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option> <option value="MGI">Organism-specific DBs - MGI</option> <option value="MIM">Organism-specific DBs - MIM</option> <option value="neXtProt">Organism-specific DBs - neXtProt</option> <option value="OpenTargets">Organism-specific DBs - OpenTargets</option> <option value="Orphanet">Organism-specific DBs - Orphanet</option> <option value="PharmGKB">Organism-specific DBs - PharmGKB</option> <option value="PomBase">Organism-specific DBs - PomBase</option> <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option> <option value="RGD">Organism-specific DBs - RGD</option> <option value="SGD">Organism-specific DBs - SGD</option> <option value="TubercuList">Organism-specific DBs - TubercuList</option> <option value="VGNC">Organism-specific DBs - VGNC</option> <option value="WormBase">Organism-specific DBs - WormBase</option> <option value="Xenbase">Organism-specific DBs - Xenbase</option> <option value="ZFIN">Organism-specific DBs - ZFIN</option> <option value="eggNOG">Phylogenomic DBs - eggNOG</option> <option value="GeneTree">Phylogenomic DBs - GeneTree</option> <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option> <option value="OMA">Phylogenomic DBs - OMA</option> <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option> <option value="TreeFam">Phylogenomic DBs - TreeFam</option> <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option> <option value="Reactome">Enzyme and pathway DBs - Reactome</option> <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option> <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option> <option value="ChiTaRS">Miscellaneous - ChiTaRS</option> <option value="GeneWiki">Miscellaneous - GeneWiki</option> <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option> <option value="PHI-base">Miscellaneous - PHI-base</option> <option value="CollecTF">Gene expression DBs - CollecTF</option> <option value="IDEAL">Family and domain DBs - IDEAL</option> <option value="DisProt">Family and domain DBs - DisProt</option> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> <option value="UniParc">UniProt - UniParc</option> <option value="UniRef50">UniProt - UniRef50</option> <option value="UniRef90">UniProt - UniRef90</option> <option value="UniRef100">UniProt - UniRef100</option> <option value="Gene_Name">UniProt - Gene Name</option> <option value="CRC64">UniProt - CRC64</option> <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option> <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option> <option value="GI_number">Sequence DBs - GI number</option> <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option> <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option> <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option> <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option> <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option> <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option> <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option> <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option> <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option> <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option> </param> </when> <when value="UniParc"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> <option value="UniParc">UniProt - UniParc</option> </param> </when> <when value="UniRef50"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> <option value="UniRef50">UniProt - UniRef50</option> </param> </when> <when value="UniRef90"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> <option value="UniRef90">UniProt - UniRef90</option> </param> </when> <when value="UniRef100"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> <option value="UniRef100">UniProt - UniRef100</option> </param> </when> <when value="Gene_Name"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="CRC64"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="CCDS"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="EMBL-GenBank-DDBJ"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="EMBL-GenBank-DDBJ_CDS"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GI_number"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PIR"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="RefSeq_Nucleotide"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="RefSeq_Protein"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PDB"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="BioGRID"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ComplexPortal"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="DIP"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="STRING"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ChEMBL"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="DrugBank"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GuidetoPHARMACOLOGY"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="SwissLipids"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Allergome"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="CLAE"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ESTHER"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="MEROPS"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PeroxiBase"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="REBASE"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="TCDB"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GlyConnect"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="BioMuta"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="DMDM"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="World-2DPAGE"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="CPTAC"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ProteomicsDB"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="DNASU"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Ensembl"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Ensembl_Genomes"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Ensembl_Genomes_Protein"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Ensembl_Genomes_Transcript"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Ensembl_Protein"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Ensembl_Transcript"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GeneID"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="KEGG"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PATRIC"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="UCSC"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="WBParaSite"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="WBParaSite_Transcript-Protein"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ArachnoServer"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Araport"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="CGD"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ConoServer"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="dictyBase"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="EchoBASE"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="euHCVdb"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="FlyBase"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GeneCards"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GeneReviews"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="HGNC"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="LegioList"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Leproma"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="MaizeGDB"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="MGI"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="MIM"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="neXtProt"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="OpenTargets"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Orphanet"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PharmGKB"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PomBase"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PseudoCAP"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="RGD"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="SGD"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="TubercuList"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="VEuPathDB"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="VGNC"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="WormBase"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="WormBase_Protein"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="WormBase_Transcript"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Xenbase"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ZFIN"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="eggNOG"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GeneTree"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="HOGENOM"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="OMA"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="OrthoDB"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="TreeFam"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="BioCyc"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PlantReactome"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="Reactome"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="UniPathway"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="ChiTaRS"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GeneWiki"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="GenomeRNAi"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="PHI-base"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="CollecTF"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="DisProt"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> <when value="IDEAL"> <param name="to" type="select" label="Target database:"> <option value="UniProtKB">UniProt - UniProtKB</option> <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> </param> </when> </conditional> </when> <when value="retrieve"> <param name="format" type="select" label="Choose format of output file" help=""> <option value="fasta">fasta</option> <option value="gff">gff</option> <option value="txt">Text</option> </param> </when> </conditional> </inputs> <outputs> <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" label="${tool.name} on ${on_string}: fasta"> <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'fasta'</filter> </data> <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output" label="${tool.name} on ${on_string}: gff"> <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'gff'</filter> </data> <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output" label="${tool.name} on ${on_string}: txt"> <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'txt'</filter> </data> <data name="outfile_map" format="tabular" from_work_dir="./output" label="${tool.name} on ${on_string}: mapping"> <filter>tool['tool_choice'] == 'map'</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="infile" value="id_uniprot.tab" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="format" value="fasta"/> <param name="tool_choice" value="retrieve"/> <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" /> </test> <test expect_num_outputs="1"> <param name="infile" value="id_uniprot.tab" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="format" value="gff"/> <param name="tool_choice" value="retrieve"/> <output name="outfile_retrieve_gff" ftype="gff"> <assert_contents> <has_n_lines min="80"/> <has_text text="UniProtKB"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="infile" value="id_uniprot.tab" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="tool_choice" value="map"/> <param name="from" value="UniProtKB_AC-ID"/> <param name="to" value="Gene_Name"/> <output name="outfile_map" file="test1_map.tab" ftype="tabular" sort="true"/> </test> <test expect_num_outputs="1"> <param name="infile" value="id_map_refseq.txt" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="tool_choice" value="map"/> <param name="from" value="RefSeq_Nucleotide"/> <param name="to" value="UniProtKB"/> <output name="outfile_map" file="test2_map.tab" ftype="tabular" sort="true"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool provides access to the UniProt API. You can retrieve sequence informations given a list of sequence identifiers or map identifiers between different databases. Hence, this tool offers you two modes: *map* and *retrieve*. ----- **INPUT** The input is a list of IDs. *Example*:: Q0P8A9 A0A077ZHN8 A0A077ZFY8 M5B8V9 M5BAG7 S0DS17 .... ----- **MAP OUTPUT EXAMPLES** FROM refseq TO embl:: From To NM_130786 A1BG_HUMAN NM_130786 V9HWD8_HUMAN NM_001087 A0A024R410_HUMAN NM_001087 AAMP_HUMAN FROM uniprot TO genename:: From To Q0P8A9 fdhC A0A077ZHN8 TTRE_0000819801 A0A077ZFY8 TTRE_0000758701 M5B8V9 CMN_01519 M5BAG7 cydC S0DS17 FFUJ_00006 A0A077Z587 TTRE_0000309301 Q13685 AAMP O14639 ABLIM1 ----- **RETRIEVE OUTPUT EXAMPLES** retrieve gff:: #gff-version 3 #sequence-region S0DS17 1 369 #sequence-region M5BAG7 1 563 #sequence-region A0A077Z587 1 772 #sequence-region A0A077ZFY8 1 973 #sequence-region O14639 1 778 O14639 UniProtKB Chain 1 778 . . . ID=PRO_0000075697;Note=Actin-binding LIM protein 1 O14639 UniProtKB Domain 97 156 . . . Note=LIM zinc-binding 1;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 O14639 UniProtKB Domain 156 216 . . . Note=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 O14639 Un... retrieve fasta:: >tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1 MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKY... >tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=3 SV=1 MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG VRAFALGRAAFRYLERITSHDAAFRALATLRV... >tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1 MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD VIKDVNGSRIDSRELCRDLIRTHKVLTV... ----- This tool is based on the work `Jan Rudolph`_ and the UniProt API. .. _Jan Rudolph: https://github.com/jdrudolph/uniprot ]]></help> <citations> <citation type="doi">10.1093/nar/gku989</citation> </citations> </tool>