uniprot_rest_interface: uniprot.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:48522382b6a4
+:cd2a41c65447
 #if $tool.tool_choice == "retrieve":
 retrieve -f $tool.format $infile ./output
 #elif $tool.tool_choice == "map":
 map
-#if $tool.from.category_FROM == "uniprot":
+#if $tool.from.category_FROM == "uniprot"
-$tool.from.db_uniprot_FROM
+'${tool.from.db_uniprot_FROM}'
-#elif $tool.from.category_FROM == "oseqdb":
+#elif $tool.from.category_FROM == "oseqdb"
-$tool.from.db_oseqdb
+${tool.from.db_oseqdb}
-#elif $tool.from.category_FROM == "3Dstrdb":
+#elif $tool.from.category_FROM == "3Dstrdb"
-$tool.from.db_3Dstrdb
+${tool.from.db_3Dstrdb}
-#elif $tool.from.category_FROM == "ppidb":
+#elif $tool.from.category_FROM == "ppidb"
-$tool.from.db_ppidb
+${tool.from.db_ppidb}
-#elif $tool.from.category_FROM == "chemistry":
+#elif $tool.from.category_FROM == "chemistry"
-$tool.from.db_chemistry
+${tool.from.db_chemistry}
-#elif $tool.from.category_FROM == "protfgdb":
+#elif $tool.from.category_FROM == "protfgdb"
-$tool.from.db_protfgdb
+${tool.from.db_protfgdb}
-#elif $tool.from.category_FROM == "polymorphismANDmutation":
+#elif $tool.from.category_FROM == "polymorphismANDmutation"
-$tool.from.db_polymorphismANDmutation
+${tool.from.db_polymorphismANDmutation}
-#elif $tool.from.category_FROM == "db_2DgelDB":
+#elif $tool.from.category_FROM == "2DgelDB"
-$tool.from.db_2DgelDB
+${tool.from.db_2DgelDB}
-#elif $tool.from.category_FROM == "ProtocolsMaterialsDB":
+#elif $tool.from.category_FROM == "ProtocolsMaterialsDB"
-$tool.from.ProtocolsMaterialsDB
+${tool.from.db_ProtocolsMaterialsDB}
-#elif $tool.from.category_FROM == "db_GenomeAnnotationDB":
+#elif $tool.from.category_FROM == "GenomeAnnotationDB"
-$tool.from.db_GenomeAnnotationDB
+${tool.from.db_GenomeAnnotationDB}
-#elif $tool.from.category_FROM == "db_OrganismSpecificGeneDB":
+#elif $tool.from.category_FROM == "OrganismSpecificGeneDB"
-$tool.from.db_OrganismSpecificGeneDB
+${tool.from.db_OrganismSpecificGeneDB}
-#elif $tool.from.category_FROM == "db_phylogenomic":
+#elif $tool.from.category_FROM == "phylogenomic"
-$tool.from.db_phylogenomic
+${tool.from.db_phylogenomic}
-#elif $tool.from.category_FROM == "db_EnzymePathwayDB":
+#elif $tool.from.category_FROM == "EnzymePathwayDB"
-$tool.from.db_EnzymePathwayDB
+${tool.from.db_EnzymePathwayDB}
-#elif $tool.from.category_FROM == "db_GeneExpression":
+#elif $tool.from.category_FROM == "GeneExpression"
-$tool.from.db_GeneExpression
+${tool.from.db_GeneExpression}
-#elif $tool.from.category_FROM == "db_other":
+#elif $tool.from.category_FROM == "other"
-$tool.from.db_other
+${tool.from.db_other}
 #end if
-#if $tool.to.category_TO == "uniprot":
+#if $tool.to.category_TO == "uniprot"
-$tool.to.db_uniprot_TO
+${tool.to.db_uniprot_TO}
-#elif $tool.to.category_TO == "oseqdb":
+#elif $tool.to.category_TO == "oseqdb"
-$tool.to.db_oseqdb
+${tool.to.db_oseqdb}
-#elif $tool.to.category_TO == "3Dstrdb":
+#elif $tool.to.category_TO == "3Dstrdb"
-$tool.to.db_3Dstrdb
+${tool.to.db_3Dstrdb}
-#elif $tool.to.category_TO == "ppidb":
+#elif $tool.to.category_TO == "ppidb"
-$tool.to.db_ppidb
+${tool.to.db_ppidb}
-#elif $tool.to.category_TO == "chemistry":
+#elif $tool.to.category_TO == "chemistry"
-$tool.to.db_chemistry
+${tool.to.db_chemistry}
-#elif $tool.to.category_TO == "protfgdb":
+#elif $tool.to.category_TO == "protfgdb"
-$tool.to.db_protfgdb
+${tool.to.db_protfgdb}
-#elif $tool.to.category_TO == "polymorphismANDmutation":
+#elif $tool.to.category_TO == "polymorphismANDmutation"
-$tool.to.db_polymorphismANDmutation
+${tool.to.db_polymorphismANDmutation}
-#elif $tool.to.category_TO == "db_2DgelDB":
+#elif $tool.to.category_TO == "2DgelDB"
-$tool.to.db_2DgelDB
+${tool.to.db_2DgelDB}
-#elif $tool.to.category_TO == "ProtocolsMaterialsDB":
+#elif $tool.to.category_TO == "ProtocolsMaterialsDB"
-$tool.to.ProtocolsMaterialsDB
+${tool.to.db_ProtocolsMaterialsDB}
-#elif $tool.to.category_TO == "db_GenomeAnnotationDB":
+#elif $tool.to.category_TO == "GenomeAnnotationDB"
-$tool.to.db_GenomeAnnotationDB
+${tool.to.db_GenomeAnnotationDB}
-#elif $tool.frtoom.category_TO == "db_OrganismSpecificGeneDB":
+#elif $tool.to.category_TO == "OrganismSpecificGeneDB"
-$tool.to.db_OrganismSpecificGeneDB
+${tool.to.db_OrganismSpecificGeneDB}
-#elif $tool.to.category_TO == "db_phylogenomic":
+#elif $tool.to.category_TO == "phylogenomic"
-$tool.to.db_phylogenomic
+${tool.to.db_phylogenomic}
-#elif $tool.to.category_TO == "db_EnzymePathwayDB":
+#elif $tool.to.category_TO == "EnzymePathwayDB"
-$tool.to.db_EnzymePathwayDB
+${tool.to.db_EnzymePathwayDB}
-#elif $tool.to.category_TO == "db_GeneExpression":
+#elif $tool.to.category_TO == "GeneExpression"
-$tool.to.db_GeneExpression
+${tool.to.db_GeneExpression}
-#elif $tool.to.category_TO == "db_other":
+#elif $tool.to.category_TO == "other"
-$tool.to.db_other
+${tool.to.db_other}
 #end if
 id_file.tabular
 ./output
 #end if
 </when>
 <when value="retrieve">
 <param name="format" type="select" label="Choose format of output file" help="">
 <option value="fasta">fasta</option>
 <option value="gff">gff</option>
+<option value="txt">Text</option>
 </param>
 </when>
 </conditional>
 </inputs>
 <outputs>
 <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
 label="${tool.name} on ${on_string} (retrieve output)">
 <filter>tool['tool_choice'] == 'retrieve'</filter>
 </data>
 <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output"
 label="${tool.name} on ${on_string} (retrieve output)">
 <filter>tool['tool_choice'] == 'retrieve'</filter>
 <filter>tool['format'] == 'gff'</filter>
+</data>
+<data name="outfile_retrieve_txt" format="txt" from_work_dir="./output"
+label="${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>
 </data>
 **INPUT**
 The input is a list of IDs.
-*example*:
+*Example*::
 Q0P8A9
 A0A077ZHN8
 A0A077ZFY8
 M5B8V9
 M5BAG7
 S0DS17
 ....
 -----
 **MAP OUTPUT EXAMPLES**

Mercurial > repos > bgruening > uniprot_rest_interface

comparison uniprot.xml @ 1:cd2a41c65447 draft