Mercurial > repos > bgruening > uniprot_rest_interface
diff uniprot.xml @ 9:468c71dac78a draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
| author | bgruening |
|---|---|
| date | Wed, 22 May 2024 21:18:15 +0000 |
| parents | af5eccf83605 |
| children |
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--- a/uniprot.xml Mon Nov 21 22:02:41 2022 +0000 +++ b/uniprot.xml Wed May 22 21:18:15 2024 +0000 @@ -1,197 +1,824 @@ -<tool id="uniprot" name="UniProt" version="0.4"> +<tool id="uniprot" name="UniProt" version="0.5" profile="23.1"> <description>ID mapping and retrieval</description> - <macros> - <import>macros.xml</import> - </macros> <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 && - '$__tool_directory__/uniprot.py' - + python '$__tool_directory__/uniprot.py' #if $tool.tool_choice == "retrieve": retrieve -f $tool.format id_file.tabular ./output #elif $tool.tool_choice == "map": map - - #if $tool.from.category_FROM == "uniprot" - '${tool.from.db_uniprot_FROM}' - #elif $tool.from.category_FROM == "oseqdb" - ${tool.from.db_oseqdb} - #elif $tool.from.category_FROM == "3Dstrdb" - ${tool.from.db_3Dstrdb} - #elif $tool.from.category_FROM == "ppidb" - ${tool.from.db_ppidb} - #elif $tool.from.category_FROM == "chemistry" - ${tool.from.db_chemistry} - #elif $tool.from.category_FROM == "protfgdb" - ${tool.from.db_protfgdb} - #elif $tool.from.category_FROM == "polymorphismANDmutation" - ${tool.from.db_polymorphismANDmutation} - #elif $tool.from.category_FROM == "2DgelDB" - ${tool.from.db_2DgelDB} - #elif $tool.from.category_FROM == "ProtocolsMaterialsDB" - ${tool.from.db_ProtocolsMaterialsDB} - #elif $tool.from.category_FROM == "GenomeAnnotationDB" - ${tool.from.db_GenomeAnnotationDB} - #elif $tool.from.category_FROM == "OrganismSpecificGeneDB" - ${tool.from.db_OrganismSpecificGeneDB} - #elif $tool.from.category_FROM == "phylogenomic" - ${tool.from.db_phylogenomic} - #elif $tool.from.category_FROM == "EnzymePathwayDB" - ${tool.from.db_EnzymePathwayDB} - #elif $tool.from.category_FROM == "GeneExpression" - ${tool.from.db_GeneExpression} - #elif $tool.from.category_FROM == "other" - ${tool.from.db_other} - #end if - - #if $tool.to.category_TO == "uniprot" - ${tool.to.db_uniprot_TO} - #elif $tool.to.category_TO == "oseqdb" - ${tool.to.db_oseqdb} - #elif $tool.to.category_TO == "3Dstrdb" - ${tool.to.db_3Dstrdb} - #elif $tool.to.category_TO == "ppidb" - ${tool.to.db_ppidb} - #elif $tool.to.category_TO == "chemistry" - ${tool.to.db_chemistry} - #elif $tool.to.category_TO == "protfgdb" - ${tool.to.db_protfgdb} - #elif $tool.to.category_TO == "polymorphismANDmutation" - ${tool.to.db_polymorphismANDmutation} - #elif $tool.to.category_TO == "2DgelDB" - ${tool.to.db_2DgelDB} - #elif $tool.to.category_TO == "ProtocolsMaterialsDB" - ${tool.to.db_ProtocolsMaterialsDB} - #elif $tool.to.category_TO == "GenomeAnnotationDB" - ${tool.to.db_GenomeAnnotationDB} - #elif $tool.to.category_TO == "OrganismSpecificGeneDB" - ${tool.to.db_OrganismSpecificGeneDB} - #elif $tool.to.category_TO == "phylogenomic" - ${tool.to.db_phylogenomic} - #elif $tool.to.category_TO == "EnzymePathwayDB" - ${tool.to.db_EnzymePathwayDB} - #elif $tool.to.category_TO == "GeneExpression" - ${tool.to.db_GeneExpression} - #elif $tool.to.category_TO == "other" - ${tool.to.db_other} - #end if - + --format tsv + "$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 name="from"> - <expand macro="macro-category_FROM"/> - <when value="uniprot"> - <expand macro="macro-db_uniprot_FROM"/> - </when> - <when value="oseqdb"> - <expand macro="macro-db_oseqdb"/> - </when> - <when value="3Dstrdb"> - <expand macro="macro-db_3Dstrdb"/> - </when> - <when value="ppidb"> - <expand macro="macro-db_ppidb"/> - </when> - <when value="chemistry"> - <expand macro="macro-db_chemistry"/> - </when> - <when value="protfgdb"> - <expand macro="macro-db_protfgdb"/> - </when> - <when value="polymorphismANDmutation"> - <expand macro="macro-db_polymorphismANDmutation"/> + <!-- 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="2DgelDB"> - <expand macro="macro-db_2DgelDB"/> + <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="ProtocolsMaterialsDB"> - <expand macro="macro-db_ProtocolsMaterialsDB"/> + <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="GenomeAnnotationDB"> - <expand macro="macro-db_GenomeAnnotationDB"/> + <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="OrganismSpecificGeneDB"> - <expand macro="macro-db_OrganismSpecificGeneDB"/> + <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="phylogenomic"> - <expand macro="macro-db_phylogenomic"/> + <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="EnzymePathwayDB"> - <expand macro="macro-db_EnzymePathwayDB"/> + <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="GeneExpression"> - <expand macro="macro-db_GeneExpression"/> + <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="other"> - <expand macro="macro-db_other"/> + <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> - </conditional> - <conditional name="to"> - <expand macro="macro-category_TO"/> - <when value="uniprot"> - <expand macro="macro-db_uniprot_TO"/> + <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="oseqdb"> - <expand macro="macro-db_oseqdb"/> + <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="3Dstrdb"> - <expand macro="macro-db_3Dstrdb"/> + <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="ppidb"> - <expand macro="macro-db_ppidb"/> + <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="chemistry"> - <expand macro="macro-db_chemistry"/> + <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="protfgdb"> - <expand macro="macro-db_protfgdb"/> + <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="polymorphismANDmutation"> - <expand macro="macro-db_polymorphismANDmutation"/> + <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="2DgelDB"> - <expand macro="macro-db_2DgelDB"/> + <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="ProtocolsMaterialsDB"> - <expand macro="macro-db_ProtocolsMaterialsDB"/> + <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="GenomeAnnotationDB"> - <expand macro="macro-db_GenomeAnnotationDB"/> + <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="OrganismSpecificGeneDB"> - <expand macro="macro-db_OrganismSpecificGeneDB"/> + <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="phylogenomic"> - <expand macro="macro-db_phylogenomic"/> + <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="EnzymePathwayDB"> - <expand macro="macro-db_EnzymePathwayDB"/> + <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="GeneExpression"> - <expand macro="macro-db_GeneExpression"/> + <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="other"> - <expand macro="macro-db_other"/> + <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> @@ -206,58 +833,54 @@ </inputs> <outputs> <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" - label="${tool.name} on ${on_string} (retrieve output)"> + label="${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 ${on_string} (retrieve output)"> + label="${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 ${on_string} (retrieve output)"> + label="${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 ${on_string} (map output)"> + label="${tool.name} on ${on_string}: mapping"> <filter>tool['tool_choice'] == 'map'</filter> </data> </outputs> <tests> - <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="fasta"/> <param name="tool_choice" value="retrieve"/> <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" /> </test> - <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" file="test2_retrieve.gff" ftype="gff" compare="sim_size" /> </test> - <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="category_FROM" value="uniprot"/> - <param name="db_uniprot_FROM" value="ID"/> - <param name="category_TO" value="uniprot"/> - <param name="db_uniprot_TO" value="GENENAME"/> + <param name="from" value="UniProtKB_AC-ID"/> + <param name="to" value="Gene_Name"/> <output name="outfile_map" file="test1_map.tab" ftype="tabular"/> </test> - <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="category_FROM" value="oseqdb"/> - <param name="db_oseqdb" value="REFSEQ_NT_ID"/> - <param name="category_TO" value="uniprot"/> - <param name="db_uniprot_TO" value="ID"/> + <param name="from" value="RefSeq_Nucleotide"/> + <param name="to" value="UniProtKB"/> <output name="outfile_map" file="test2_map.tab" ftype="tabular"/> </test> </tests>