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irida_workflow_structure.ga
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/
irida_workflow_structure.ga
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{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "Read info",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "sequence_reads"
}
],
"label": null,
"name": "Input dataset collection",
"outputs": [],
"position": {
"left": 200,
"top": 200
},
"tool_errors": null,
"tool_id": null,
"tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"sequence_reads\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "e267248b-6ddc-4b5e-a476-e805ce1bc4d5",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "ae59d874-94ab-4b14-b456-15e2fee2860d"
}
]
},
"1": {
"annotation": "",
"content_id": "__UNZIP_COLLECTION__",
"id": 1,
"input_connections": {
"input": {
"id": 0,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Unzip Collection",
"name": "input"
}
],
"label": null,
"name": "Unzip Collection",
"outputs": [
{
"name": "forward",
"type": "data"
},
{
"name": "reverse",
"type": "data"
}
],
"position": {
"left": 464,
"top": 200
},
"post_job_actions": {
"HideDatasetActionforward": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "forward"
},
"HideDatasetActionreverse": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "reverse"
}
},
"tool_errors": null,
"tool_id": "__UNZIP_COLLECTION__",
"tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "a4a5c3fa-9825-436e-b58f-5874c9419a73",
"workflow_outputs": []
},
"2": {
"annotation": "",
"content_id": "cat1",
"id": 2,
"input_connections": {
"input1": {
"id": 1,
"output_name": "forward"
},
"queries_0|input2": {
"id": 1,
"output_name": "reverse"
}
},
"inputs": [
{
"description": "runtime parameter for tool Concatenate datasets",
"name": "input1"
}
],
"label": null,
"name": "Concatenate datasets",
"outputs": [
{
"name": "out_file1",
"type": "input"
}
],
"position": {
"left": 693,
"top": 200
},
"post_job_actions": {
"HideDatasetActionout_file1": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "out_file1"
}
},
"tool_errors": null,
"tool_id": "cat1",
"tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"queries\": \"[{\\\"input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__index__\\\": 0}]\"}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "063e50a7-613b-490a-8c95-c11502b4eef3",
"workflow_outputs": []
},
"3": {
"annotation": "",
"content_id": "secure_hash_message_digest",
"id": 3,
"input_connections": {
"input1": {
"id": 2,
"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Secure Hash / Message Digest",
"name": "input1"
}
],
"label": null,
"name": "Secure Hash / Message Digest",
"outputs": [
{
"name": "out_file1",
"type": "tabular"
}
],
"position": {
"left": 951,
"top": 200
},
"post_job_actions": {
"RenameDatasetActionout_file1": {
"action_arguments": {
"newname": "hash.txt"
},
"action_type": "RenameDatasetAction",
"output_name": "out_file1"
}
},
"tool_errors": null,
"tool_id": "secure_hash_message_digest",
"tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"algorithms\": \"[\\\"md5\\\", \\\"sha1\\\"]\"}",
"tool_version": "0.0.1",
"type": "tool",
"uuid": "89d3c371-d9c2-46b1-997e-32111e2d8eb8",
"workflow_outputs": [
{
"label": null,
"output_name": "out_file1",
"uuid": "80f7f94f-d17f-4901-983b-0a425558a735"
}
]
},
"4": {
"annotation": "",
"content_id": "Grep1",
"id": 4,
"input_connections": {
"input": {
"id": 2,
"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Select",
"name": "input"
}
],
"label": null,
"name": "Select",
"outputs": [
{
"name": "out_file1",
"type": "input"
}
],
"position": {
"left": 951,
"top": 318
},
"post_job_actions": {
"HideDatasetActionout_file1": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "out_file1"
}
},
"tool_errors": null,
"tool_id": "Grep1",
"tool_state": "{\"__page__\": 0, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"pattern\": \"\\\"^@\\\"\"}",
"tool_version": "1.0.1",
"type": "tool",
"uuid": "60285382-ae86-459d-a12e-92802a42d609",
"workflow_outputs": []
},
"5": {
"annotation": "",
"content_id": "wc_gnu",
"id": 5,
"input_connections": {
"input1": {
"id": 4,
"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Line/Word/Character count",
"name": "input1"
}
],
"label": null,
"name": "Line/Word/Character count",
"outputs": [
{
"name": "out_file1",
"type": "tabular"
}
],
"position": {
"left": 1258,
"top": 200
},
"post_job_actions": {
"RenameDatasetActionout_file1": {
"action_arguments": {
"newname": "read-count.txt"
},
"action_type": "RenameDatasetAction",
"output_name": "out_file1"
}
},
"tool_errors": null,
"tool_id": "wc_gnu",
"tool_state": "{\"__page__\": 0, \"include_header\": \"\\\"false\\\"\", \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "ad321335-c1b4-4fdd-959b-dcef38933925",
"workflow_outputs": [
{
"label": null,
"output_name": "out_file1",
"uuid": "227d5587-f089-488c-b228-c92bde3de17d"
}
]
}
},
"uuid": "0c442c06-8fd2-4a42-b8a2-9585b30deb43"
}