| 
0
 | 
     1 {
 | 
| 
 | 
     2     "a_galaxy_workflow": "true", 
 | 
| 
 | 
     3     "annotation": "{\n  \"description\": \"Merge a list of BAM files into a single BAM.\",\n  \"file_relationship\": {\n    \"file_relationship\": {},\n    \"value_type\": \"LIST\",\n    \"name\": \"List of BAM Files\",\n    \"input_files\": [\n      {\n        \"allowed_filetypes\": [{\"name\": \"BAM\"}],\n        \"name\": \"Input File\",\n        \"description\": \"File to be merged\"\n      }\n    ]\n  }\n}", 
 | 
| 
 | 
     4     "format-version": "0.1", 
 | 
| 
 | 
     5     "name": "Merge BAM", 
 | 
| 
 | 
     6     "steps": {
 | 
| 
 | 
     7         "0": {
 | 
| 
 | 
     8             "annotation": "", 
 | 
| 
 | 
     9             "content_id": null, 
 | 
| 
 | 
    10             "id": 0, 
 | 
| 
 | 
    11             "input_connections": {}, 
 | 
| 
 | 
    12             "inputs": [
 | 
| 
 | 
    13                 {
 | 
| 
 | 
    14                     "description": "", 
 | 
| 
 | 
    15                     "name": "Input Dataset Collection"
 | 
| 
 | 
    16                 }
 | 
| 
 | 
    17             ], 
 | 
| 
 | 
    18             "label": null, 
 | 
| 
 | 
    19             "name": "Input dataset collection", 
 | 
| 
 | 
    20             "outputs": [], 
 | 
| 
 | 
    21             "position": {
 | 
| 
 | 
    22                 "left": 200.5, 
 | 
| 
 | 
    23                 "top": 284.5
 | 
| 
 | 
    24             }, 
 | 
| 
 | 
    25             "tool_errors": null, 
 | 
| 
 | 
    26             "tool_id": null, 
 | 
| 
 | 
    27             "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", 
 | 
| 
 | 
    28             "tool_version": null, 
 | 
| 
 | 
    29             "type": "data_collection_input", 
 | 
| 
 | 
    30             "uuid": "d9e52442-15c8-45ba-a07e-fdf9de76ac43", 
 | 
| 
 | 
    31             "workflow_outputs": [
 | 
| 
 | 
    32                 {
 | 
| 
 | 
    33                     "label": null, 
 | 
| 
 | 
    34                     "output_name": "output", 
 | 
| 
 | 
    35                     "uuid": "463f98ce-580f-4a70-8d89-1be510478bb9"
 | 
| 
 | 
    36                 }
 | 
| 
 | 
    37             ]
 | 
| 
 | 
    38         }, 
 | 
| 
 | 
    39         "1": {
 | 
| 
 | 
    40             "annotation": "", 
 | 
| 
 | 
    41             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0", 
 | 
| 
 | 
    42             "id": 1, 
 | 
| 
 | 
    43             "input_connections": {
 | 
| 
 | 
    44                 "inputFile": {
 | 
| 
 | 
    45                     "id": 0, 
 | 
| 
 | 
    46                     "output_name": "output"
 | 
| 
 | 
    47                 }
 | 
| 
 | 
    48             }, 
 | 
| 
 | 
    49             "inputs": [], 
 | 
| 
 | 
    50             "label": null, 
 | 
| 
 | 
    51             "name": "MergeSamFiles", 
 | 
| 
 | 
    52             "outputs": [
 | 
| 
 | 
    53                 {
 | 
| 
 | 
    54                     "name": "outFile", 
 | 
| 
 | 
    55                     "type": "bam"
 | 
| 
 | 
    56                 }
 | 
| 
 | 
    57             ], 
 | 
| 
 | 
    58             "position": {
 | 
| 
 | 
    59                 "left": 575, 
 | 
| 
 | 
    60                 "top": 285
 | 
| 
 | 
    61             }, 
 | 
| 
 | 
    62             "post_job_actions": {
 | 
| 
 | 
    63                 "RenameDatasetActionoutFile": {
 | 
| 
 | 
    64                     "action_arguments": {
 | 
| 
 | 
    65                         "newname": "merged"
 | 
| 
 | 
    66                     }, 
 | 
| 
 | 
    67                     "action_type": "RenameDatasetAction", 
 | 
| 
 | 
    68                     "output_name": "outFile"
 | 
| 
 | 
    69                 }
 | 
| 
 | 
    70             }, 
 | 
| 
 | 
    71             "tool_errors": null, 
 | 
| 
 | 
    72             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0", 
 | 
| 
 | 
    73             "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"merge_sequence_dictionaries\": \"\\\"False\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\", \"inputFile\": \"null\"}", 
 | 
| 
 | 
    74             "tool_version": "1.126.0", 
 | 
| 
 | 
    75             "type": "tool", 
 | 
| 
 | 
    76             "uuid": "0f22ffbb-d375-4d1f-9b53-0abce7390f66", 
 | 
| 
 | 
    77             "workflow_outputs": [
 | 
| 
 | 
    78                 {
 | 
| 
 | 
    79                     "label": null, 
 | 
| 
 | 
    80                     "output_name": "outFile", 
 | 
| 
 | 
    81                     "uuid": "82e3ef46-e532-4e2f-bafb-f0875211282f"
 | 
| 
 | 
    82                 }
 | 
| 
 | 
    83             ]
 | 
| 
 | 
    84         }
 | 
| 
 | 
    85     }, 
 | 
| 
 | 
    86     "uuid": "a920711d-9852-4048-9694-eda710a7513a"
 | 
| 
 | 
    87 } |