Mercurial > repos > bgruening > uniprot_rest_interface
diff uniprot.xml @ 1:cd2a41c65447 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489
| author | bgruening |
|---|---|
| date | Fri, 14 Oct 2016 17:59:02 -0400 |
| parents | 48522382b6a4 |
| children | fe94765e8814 |
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--- a/uniprot.xml Fri Oct 09 16:42:22 2015 -0400 +++ b/uniprot.xml Fri Oct 14 17:59:02 2016 -0400 @@ -24,68 +24,68 @@ #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 == "db_2DgelDB": - $tool.from.db_2DgelDB - #elif $tool.from.category_FROM == "ProtocolsMaterialsDB": - $tool.from.ProtocolsMaterialsDB - #elif $tool.from.category_FROM == "db_GenomeAnnotationDB": - $tool.from.db_GenomeAnnotationDB - #elif $tool.from.category_FROM == "db_OrganismSpecificGeneDB": - $tool.from.db_OrganismSpecificGeneDB - #elif $tool.from.category_FROM == "db_phylogenomic": - $tool.from.db_phylogenomic - #elif $tool.from.category_FROM == "db_EnzymePathwayDB": - $tool.from.db_EnzymePathwayDB - #elif $tool.from.category_FROM == "db_GeneExpression": - $tool.from.db_GeneExpression - #elif $tool.from.category_FROM == "db_other": - $tool.from.db_other + #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 == "db_2DgelDB": - $tool.to.db_2DgelDB - #elif $tool.to.category_TO == "ProtocolsMaterialsDB": - $tool.to.ProtocolsMaterialsDB - #elif $tool.to.category_TO == "db_GenomeAnnotationDB": - $tool.to.db_GenomeAnnotationDB - #elif $tool.frtoom.category_TO == "db_OrganismSpecificGeneDB": - $tool.to.db_OrganismSpecificGeneDB - #elif $tool.to.category_TO == "db_phylogenomic": - $tool.to.db_phylogenomic - #elif $tool.to.category_TO == "db_EnzymePathwayDB": - $tool.to.db_EnzymePathwayDB - #elif $tool.to.category_TO == "db_GeneExpression": - $tool.to.db_GeneExpression - #elif $tool.to.category_TO == "db_other": - $tool.to.db_other + #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" + ${tool.to.db_other} #end if id_file.tabular @@ -205,10 +205,10 @@ <param name="format" type="select" label="Choose format of output file" help=""> <option value="fasta">fasta</option> <option value="gff">gff</option> + <option value="txt">Text</option> </param> </when> </conditional> - </inputs> <outputs> <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" @@ -221,6 +221,11 @@ <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'gff'</filter> </data> + <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output" + label="${tool.name} on ${on_string} (retrieve output)"> + <filter>tool['tool_choice'] == 'retrieve'</filter> + <filter>tool['format'] == 'txt'</filter> + </data> <data name="outfile_map" format="tabular" from_work_dir="./output" label="${tool.name} on ${on_string} (map output)"> <filter>tool['tool_choice'] == 'map'</filter> @@ -278,15 +283,15 @@ The input is a list of IDs. -*example*: +*Example*:: -Q0P8A9 -A0A077ZHN8 -A0A077ZFY8 -M5B8V9 -M5BAG7 -S0DS17 -.... + Q0P8A9 + A0A077ZHN8 + A0A077ZFY8 + M5B8V9 + M5BAG7 + S0DS17 + .... -----