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tools.json
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tools.json
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{
"_id" : "tool_skeleton",
"name" : "Tool Skeleton",
"title" : "Tool Skeleton Template",
"short_description" : "Skeleton for a VRE tool definition",
"long_description" : "This a a longer description on what this tool is about: a dummy application for demonstration purposes only.",
"url" : "https://github.com/tool_skelon/VREwrapping",
"publication" : "10.00000/if-any",
"owner" : {
"author" : "Your Name",
"institution" : "Your institution",
"contact" : "Your email account"
},
"status" : 1,
"external" : true,
"keywords" : [
"next gen seq",
"dna"
],
"keywords_tool" : [
"Tool skeleton",
"Sample keyword"
],
"infrastructure" : {
"memory" : 12.0,
"cpus" : 4.0,
"executable" : "/remote/host/path/for/dummy/tool_skeleton/wrapper.py",
"clouds" : {
"life-bsc" : {
"launcher" : "SGE",
"queue" : "default.q"
},
"life-bsc2" : {
"launcher" : "PMES",
"workflowType" : "COMPSs",
"minimumVMs" : 1.0,
"initialVMs" : 1.0,
"imageName" : "uuid_tool_skeleton_image_00",
"default_cloud" : false
}
}
},
"input_files" : [
{
"name" : "fasta1",
"description" : "FASTA input file 1",
"help" : "This is the input file 1 help tooltip",
"file_type" : [
"FASTA"
],
"data_type" : [
"dna_sequence"
],
"required" : true,
"allow_multiple" : false
},
{
"name" : "fasta2",
"description" : "FASTA input file 2",
"help" : "This is the input file 2 help tooltip",
"file_type" : [
"FASTA"
],
"data_type" : [
"dna_sequence"
],
"required" : false,
"allow_multiple" : false
}
],
"input_files_combinations" : [
{
"description" : "Start tool with 1 FASTA FILE",
"input_files" : [
"fasta1"
]
},
{
"description" : "Start tool with 2 FASTA FILES",
"input_files" : [
"fasta1",
"fasta2"
]
}
],
"input_files_combinations_internal" : [
[
{
"dna_sequence" : 1
},
{
"dna_sequence" : 1
}
],
[
{
"dna_sequence" : 1
}
]
],
"arguments" : [
{
"name" : "1_arg_boolean",
"description" : "Argument 1 Boolean",
"help" : " Tooltip for this argument",
"type" : "boolean",
"default" : "false"
},
{
"name" : "2_arg_enum_mult",
"description" : "Argument 2 Enum Multiple",
"help" : " Tooltip for this argument",
"type" : "enum_multiple",
"enum_items" : {
"name" : [
"option 1 name",
"option 2 name"
],
"description" : [
"option1",
"option2"
]
},
"required" : true,
"default" : ""
},
{
"name" : "3_arg_integer",
"description" : "Argument 3 Integer",
"help" : " Tooltip for this argument",
"type" : "integer",
"minimum" : 1,
"maximum" : 500,
"required" : true,
"default" : "100"
},
{
"name" : "4_arg_string",
"description" : "Argument 4 String",
"help" : " Tooltip for this argument",
"type" : "string",
"required" : true,
"allow_multiple" : false
}
],
"has_custom_viewer" : false,
"output_files" : [
{
"name" : "output1",
"required" : true,
"allow_multiple" : false,
"file" : {
"file_type" : "FASTA",
"data_type" : "dna_sequence",
"meta_data" : {
"visible" : true,
"description" : "Output File 1 description"
}
}
}
]
}
{
"_id" : "wget",
"title" : "Remote file retrieving from URLs",
"name" : "Get remote file",
"short_description" : "Implementation of a the remote file retriever WGET.",
"url" : "https://www.gnu.org/software/wget/",
"owner" : {
"institution" : "Barcelona Supercomputing Center",
"author" : "Laia Codo",
"contact" : "[email protected]",
"url" : "",
"user" : "[email protected]"
},
"external" : false,
"keywords" : [
],
"infrastructure" : {
"memory" : "",
"cpus" : 1,
"executable" : "/ABSOLUTE/PATH/TO/VRE/DATA/apps/localTools/wget/wget.sh",
"clouds" : {
"mug-bsc" : {
"launcher" : "SGE",
"queue" : "local.q"
}
}
},
"input_files" : [
],
"arguments" : [
{
"name" : "url",
"description" : "URL of the file to be downloaded",
"help" : "URL",
"type" : "string",
"required" : true,
"allow_multiple" : true
},
{
"name" : "output",
"description" : "Name of the output file",
"help" : "Name of the output file",
"type" : "string",
"allow_multiple" : false,
"default" : ""
},
{
"name" : "working_dir",
"description" : "Temporal dir",
"help" : "",
"type" : "string",
"allow_multiple" : false,
"default" : ""
},
{
"name" : "untar",
"description" : "Untar output file if ",
"help" : "",
"type" : "string",
"allow_multiple" : false,
"default" : ""
}
],
"control_file" : ".summary.json",
"output_files" : [
{
"name" : "file",
"required" : true,
"allow_multiple" : false,
"file_type" : "",
"data_type" : "",
"file" : {
"meta_data" : {
"validated" : false,
"description" : "Data imported from URL",
"tool" : "wget",
"visible" : true
}
}
}
]
}