Mercurial > repos > kyost > atac_primer_tool

annotate ATAC_Primer_Tool.ga @ 3:fbfe7b785ea7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add test for 0 standard deviation.
author kyost
date Wed, 02 May 2018 13:20:01 -0400
parents fd3ea97a96bc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
1 {"uuid": "adf14070-f445-41b0-ba62-c9a96d71bae5", "tags": [], "format-version": "0.1", "name": "ATAC Primer Tool", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "4a35572c-71e7-4459-8588-5f5934dfa525", "label": null}], "input_connections": {}, "tool_state": "{\"collection_type\": \"list\"}", "id": 0, "uuid": "2c0a2479-903a-46d6-af83-2fd16f0c4111", "errors": null, "name": "Input dataset collection", "label": "ATAC-seq bam files", "inputs": [], "position": {"top": 294, "left": 214}, "annotation": "", "content_id": null, "type": "data_collection_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "cb2d4088-fe8d-454b-aea3-118709f04e53", "label": null}], "input_connections": {}, "tool_state": "{}", "id": 1, "uuid": "0b108843-4679-4a27-b45c-2aeb734f4659", "errors": null, "name": "Input dataset", "label": "chrom.sizes", "inputs": [], "position": {"top": 449.5, "left": 198}, "annotation": "", "content_id": null, "type": "data_input"}, "2": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "1a1ce0ab-0645-49c8-a41c-fce53509282d", "label": null}], "input_connections": {}, "tool_state": "{}", "id": 2, "uuid": "6c0d911c-ebb7-416e-ac79-8a5e003d7887", "errors": null, "name": "Input dataset", "label": "Peak bed file", "inputs": [], "position": {"top": 593, "left": 140.5}, "annotation": "", "content_id": null, "type": "data_input"}, "3": {"tool_id": "filter_bam", "tool_version": "0.1.0", "outputs": [{"type": "bed", "name": "output1"}, {"type": "bam", "name": "output2"}, {"type": "tabular", "name": "output3"}], "workflow_outputs": [], "input_connections": {"input2": {"output_name": "output", "id": 2}, "input3": {"output_name": "output", "id": 1}, "input1": {"output_name": "output", "id": 0}}, "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input3\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}", "id": 3, "uuid": "cf3b0244-7460-4d59-a0ef-c74f3b1e0a41", "errors": null, "name": "Filter bam files", "post_job_actions": {"HideDatasetActionoutput3": {"output_name": "output3", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput2": {"output_name": "output2", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput1": {"output_name": "output1", "action_type": "HideDatasetAction", "action_arguments": {}}, "RenameDatasetActionoutput2": {"output_name": "output2", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "#{input1 | basename}.filter.bam"}}}, "label": null, "inputs": [{"name": "input2", "description": "runtime parameter for tool Filter bam files"}, {"name": "input3", "description": "runtime parameter for tool Filter bam files"}, {"name": "input1", "description": "runtime parameter for tool Filter bam files"}], "position": {"top": 364.5, "left": 554}, "annotation": "", "content_id": "filter_bam", "type": "tool"}, "4": {"tool_id": "make_window_bed", "tool_version": "0.1.0", "outputs": [{"type": "bed", "name": "output"}], "workflow_outputs": [], "input_connections": {"input1": {"output_name": "output", "id": 2}}, "tool_state": "{\"input2\": \"\\\"100\\\"\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"galaxy_input2\": \"\\\"100\\\"\", \"galaxy_input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null}", "id": 4, "uuid": "bcd18c7c-9923-4f61-866a-65242eb0a3b2", "errors": null, "name": "Create bed file of qPCR windows", "post_job_actions": {"RenameDatasetActiongalaxy_output": {"output_name": "galaxy_output", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "qPCR window bed file"}}, "HideDatasetActionoutput": {"output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": "Create bed file of qPCR windows", "inputs": [{"name": "input1", "description": "runtime parameter for tool Create bed file of qPCR windows"}], "position": {"top": 637.5, "left": 479.5}, "annotation": "", "content_id": "make_window_bed", "type": "tool"}, "5": {"tool_id": "concatenate_ordered", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "output1"}], "workflow_outputs": [], "input_connections": {"input1": {"output_name": "output3", "id": 3}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 5, "uuid": "1aa966bb-d26e-4a42-ba94-13683bfe07d9", "errors": null, "name": "Concatenate Ordered Dataset Collection", "post_job_actions": {"HideDatasetActionoutput1": {"output_name": "output1", "action_type": "HideDatasetAction", "action_arguments": {}}, "RenameDatasetActionoutput1": {"output_name": "output1", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "read_counts.txt"}}}, "label": null, "inputs": [{"name": "input1", "description": "runtime parameter for tool Concatenate Ordered Dataset Collection"}], "position": {"top": 387, "left": 866.5}, "annotation": "", "content_id": "concatenate_ordered", "type": "tool"}, "6": {"tool_id": "window_coverage", "tool_version": "0.1.0", "outputs": [{"type": "bed", "name": "output1"}, {"type": "bed", "name": "output2"}], "workflow_outputs": [], "input_connections": {"input2": {"output_name": "output", "id": 4}, "input1": {"output_name": "output2", "id": 3}}, "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input3\": \"\\\"0.9\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}", "id": 6, "uuid": "2edcc6f7-3942-481b-b81d-35cb7ddc04c6", "errors": null, "name": "Calculate window coverage", "post_job_actions": {"HideDatasetActionoutput2": {"output_name": "output2", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput1": {"output_name": "output1", "action_type": "HideDatasetAction", "action_arguments": {}}, "RenameDatasetActionoutput2": {"output_name": "output2", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "Spanning fragment coverage bed file"}}, "RenameDatasetActionoutput1": {"output_name": "output1", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "Coverage bed file"}}}, "label": null, "inputs": [{"name": "input2", "description": "runtime parameter for tool Calculate window coverage"}, {"name": "input1", "description": "runtime parameter for tool Calculate window coverage"}], "position": {"top": 654.5, "left": 895}, "annotation": "", "content_id": "window_coverage", "type": "tool"}, "7": {"tool_id": "find_qPCR_regions", "tool_version": "0.1.0", "outputs": [{"type": "bed", "name": "output"}], "workflow_outputs": [{"output_name": "galaxy_output", "uuid": "f600b360-070e-4575-ac5d-f04c91b39dd3", "label": null}, {"output_name": "output", "uuid": "fff2624f-b80a-41d7-9266-7f045dbeada7", "label": "ATAC qPCR regions"}], "input_connections": {"input2": {"output_name": "output2", "id": 6}, "input3": {"output_name": "output1", "id": 5}, "input1": {"output_name": "output1", "id": 6}}, "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input3\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input4\": \"\\\"0.8\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input5\": \"\\\"3\\\"\"}", "id": 7, "uuid": "24038597-f150-48f0-9d82-780c5a365649", "errors": null, "name": "Find ATAC qPCR regions", "post_job_actions": {"RenameDatasetActionoutput": {"output_name": "output", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "ATAC qPCR regions"}}}, "label": "Find ATAC qPCR regions", "inputs": [{"name": "input2", "description": "runtime parameter for tool Find ATAC qPCR regions"}, {"name": "input3", "description": "runtime parameter for tool Find ATAC qPCR regions"}, {"name": "input1", "description": "runtime parameter for tool Find ATAC qPCR regions"}], "position": {"top": 521.5, "left": 1240.5}, "annotation": "", "content_id": "find_qPCR_regions", "type": "tool"}, "8": {"tool_id": "Extract genomic DNA 1", "tool_version": "2.2.3", "outputs": [{"type": "input", "name": "out_file1"}], "workflow_outputs": [{"output_name": "out_file1", "uuid": "b77e473a-edfd-41b2-b042-309282512b26", "label": "ATAC qPCR regions sequences"}], "input_connections": {"input": {"output_name": "output", "id": 7}}, "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"interpret_features\": \"\\\"yes\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 8, "uuid": "1cb77694-0165-4eba-a5d5-03cade8c8c60", "errors": null, "name": "Extract Genomic DNA", "post_job_actions": {"RenameDatasetActionout_file1": {"output_name": "out_file1", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "ATAC qPCR regions DNA sequences"}}}, "label": "Extract DNA sequence for ATAC qPCR Regions", "inputs": [{"name": "input", "description": "runtime parameter for tool Extract Genomic DNA"}], "position": {"top": 534, "left": 1548}, "annotation": "", "content_id": "Extract genomic DNA 1", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}