Mercurial > repos > artbio > metavisitor_2_workflows
view Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga @ 0:c375489bbcb0 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows/metavisitor_2_workflows commit ecf95caa7d5e9ab001a75cbf5fb306e7ecd3def3
author | artbio |
---|---|
date | Sun, 21 Jul 2019 19:22:52 -0400 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "uuid": "64d78b22-76ae-49d2-a851-a9dcdca491b4", "tags": [], "format-version": "0.1", "version": 4, "steps": { "1": { "tool_id": null, "errors": null, "uuid": "e8e196c7-c854-4bd9-ace2-345a0d797090", "tool_version": null, "outputs": [], "workflow_outputs": [ { "output_name": "output", "uuid": "46b1caea-3a7c-4663-b2e1-6536a346567a", "label": null } ], "annotation": "", "content_id": null, "input_connections": {}, "inputs": [ { "name": "Nora Virus Genomes", "description": "" } ], "position": { "top": 474.5333251953125, "left": 634.5333251953125 }, "tool_state": "{\"collection_type\": \"list\", \"name\": \"Nora Virus Genomes\"}", "label": "Nora Virus Genomes", "type": "data_collection_input", "id": 1, "name": "Input dataset collection" }, "0": { "tool_id": null, "errors": null, "uuid": "ca202c6a-46b7-4f3a-a2ab-dbc781f331b7", "tool_version": null, "outputs": [], "workflow_outputs": [ { "output_name": "output", "uuid": "19eaa717-5b9a-4b27-a1c4-a895fc673970", "label": null } ], "annotation": "", "content_id": null, "input_connections": {}, "inputs": [ { "name": "Read fastq files", "description": "" } ], "position": { "top": 269.51666259765625, "left": 199.5333251953125 }, "tool_state": "{\"collection_type\": \"list\", \"name\": \"Read fastq files\"}", "label": "Read fastq files", "type": "data_collection_input", "id": 0, "name": "Input dataset collection" }, "3": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", "errors": null, "uuid": "b0f07d5d-ce07-4fba-b8c6-9ad6502e0aa9", "tool_version": "1.4.1", "outputs": [ { "type": "input", "name": "paired_output" }, { "type": "input", "name": "list_output" }, { "type": "input", "name": "out_file1" }, { "type": "_sniff_", "name": "paired_out_file" } ], "post_job_actions": { "RenameDatasetActionout_file1": { "output_name": "out_file1", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Concatenated genome files" } }, "HideDatasetActionpaired_output": { "output_name": "paired_output", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionout_file1": { "output_name": "out_file1", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionlist_output": { "output_name": "list_output", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [ { "output_name": "paired_out_file", "uuid": "66775d63-ac73-47b2-a9a3-736247d43bed", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", "input_connections": { "global_condition|inputs": { "output_name": "output", "id": 1 } }, "inputs": [ { "name": "global_condition", "description": "runtime parameter for tool Concatenate multiple datasets" } ], "position": { "top": 600.5, "left": 862 }, "tool_state": "{\"dataset_names\": \"\\\"false\\\"\", \"headers\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"global_condition\": \"{\\\"__current_case__\\\": 0, \\\"input_type\\\": \\\"singles\\\", \\\"inputs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", "label": "Concatenat genome files", "type": "tool", "id": 3, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "55cf9d9defd1", "name": "concatenate_multiple_datasets", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Concatenate multiple datasets" }, "2": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/yac_clipper/yac/2.3.0", "errors": null, "uuid": "afa187ce-544c-4287-8699-a9efe8ce45ab", "tool_version": "2.3.0", "outputs": [ { "type": "input", "name": "output" } ], "post_job_actions": { "HideDatasetActionoutput": { "output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionoutput": { "output_name": "output", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "#{input} clipped" } } }, "workflow_outputs": [], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/yac_clipper/yac/2.3.0", "input_connections": { "input": { "output_name": "output", "id": 0 } }, "inputs": [ { "name": "input", "description": "runtime parameter for tool Clip adapter" } ], "position": { "top": 414.5333251953125, "left": 384.51666259765625 }, "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": null, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"clip_source\": \"{\\\"__current_case__\\\": 0, \\\"clip_sequence\\\": \\\"CTGTAGGCACCATCAATCGT\\\", \\\"clip_source_list\\\": \\\"prebuilt\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"Nmode\": \"\\\"reject\\\"\"}", "label": null, "type": "tool", "id": 2, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "f7947c5a18b8", "name": "yac_clipper", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Clip adapter" }, "5": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", "errors": null, "uuid": "41517d42-910e-416b-99a4-b307a58be294", "tool_version": "2.1.1", "outputs": [ { "type": "tabular", "name": "output" }, { "type": "input", "name": "aligned" }, { "type": "input", "name": "unaligned" } ], "post_job_actions": { "HideDatasetActionunaligned": { "output_name": "unaligned", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionaligned": { "output_name": "aligned", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput": { "output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [], "annotation": "Align reads to the different nora genomes to get some stats", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", "input_connections": { "input": { "output_name": "out_file1", "id": 4 }, "refGenomeSource|ownFile": { "output_name": "output", "id": 1 } }, "inputs": [ { "name": "input", "description": "runtime parameter for tool sR_bowtie" }, { "name": "refGenomeSource", "description": "runtime parameter for tool sR_bowtie" } ], "position": { "top": 170, "left": 924 }, "tool_state": "{\"__page__\": null, \"output_format\": \"\\\"tabular\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"additional_fasta\": \"\\\"No\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"method\": \"\\\"multiple\\\"\"}", "label": "Align reads to Nora genomes", "type": "tool", "id": 5, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "0281bb245635", "name": "sr_bowtie", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "sR_bowtie" }, "4": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", "errors": null, "uuid": "ed4ab4ea-bc94-4fb4-8300-93d842b10ba4", "tool_version": "1.4.1", "outputs": [ { "type": "input", "name": "paired_output" }, { "type": "input", "name": "list_output" }, { "type": "input", "name": "out_file1" }, { "type": "_sniff_", "name": "paired_out_file" } ], "post_job_actions": { "HideDatasetActionpaired_out_file": { "output_name": "paired_out_file", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionout_file1": { "output_name": "out_file1", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "#{global_condition.inputs}" } }, "HideDatasetActionpaired_output": { "output_name": "paired_output", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionlist_output": { "output_name": "list_output", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [ { "output_name": "out_file1", "uuid": "7df3805f-edaa-4ab4-adf8-8e21f83b4e99", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", "input_connections": { "global_condition|inputs": { "output_name": "output", "id": 2 } }, "inputs": [ { "name": "global_condition", "description": "runtime parameter for tool Concatenate multiple datasets" } ], "position": { "top": 214.5, "left": 584 }, "tool_state": "{\"dataset_names\": \"\\\"false\\\"\", \"headers\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"global_condition\": \"{\\\"__current_case__\\\": 0, \\\"input_type\\\": \\\"singles\\\", \\\"inputs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", "label": "Concatenate read files", "type": "tool", "id": 4, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "55cf9d9defd1", "name": "concatenate_multiple_datasets", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Concatenate multiple datasets" }, "7": { "tool_id": "wc_gnu", "errors": null, "uuid": "c8a5c107-93fc-4e16-bd42-cd86efdbd79a", "tool_version": "1.0.0", "outputs": [ { "type": "tabular", "name": "out_file1" } ], "post_job_actions": { "RenameDatasetActionout_file1": { "output_name": "out_file1", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "nbre of remapped reads" } } }, "workflow_outputs": [ { "output_name": "out_file1", "uuid": "b773db8b-eefc-4d13-8402-4f419883370b", "label": null } ], "annotation": "", "content_id": "wc_gnu", "input_connections": { "input1": { "output_name": "output", "id": 5 } }, "inputs": [ { "name": "input1", "description": "runtime parameter for tool Line/Word/Character count" } ], "position": { "top": 308, "left": 1292.5 }, "tool_state": "{\"__page__\": null, \"include_header\": \"\\\"true\\\"\", \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}", "label": null, "type": "tool", "id": 7, "name": "Line/Word/Character count" }, "6": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", "errors": null, "uuid": "60a797b5-2583-403f-89ed-da90913b6039", "tool_version": "2.1.1", "outputs": [ { "type": "tabular", "name": "output" }, { "type": "input", "name": "aligned" }, { "type": "input", "name": "unaligned" } ], "post_job_actions": { "HideDatasetActionunaligned": { "output_name": "unaligned", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput": { "output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionaligned": { "output_name": "aligned", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", "input_connections": { "input": { "output_name": "out_file1", "id": 4 }, "refGenomeSource|ownFile": { "output_name": "out_file1", "id": 3 } }, "inputs": [ { "name": "input", "description": "runtime parameter for tool sR_bowtie" }, { "name": "refGenomeSource", "description": "runtime parameter for tool sR_bowtie" } ], "position": { "top": 529, "left": 1285 }, "tool_state": "{\"__page__\": null, \"output_format\": \"\\\"bam\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"additional_fasta\": \"\\\"No\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"method\": \"\\\"a_option\\\"\"}", "label": "Align reads to genomes", "type": "tool", "id": 6, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "0281bb245635", "name": "sr_bowtie", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "sR_bowtie" }, "8": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/small_rna_maps/small_rna_maps/2.14.0", "errors": null, "uuid": "42bcdda1-209a-43d2-a5aa-2c02d1665d07", "tool_version": "2.14.0", "outputs": [ { "type": "tabular", "name": "output_tab" }, { "type": "bed", "name": "output_bed" }, { "type": "tabular", "name": "extra_output_tab" }, { "type": "pdf", "name": "output_pdf" } ], "post_job_actions": { "HideDatasetActionextra_output_tab": { "output_name": "extra_output_tab", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput_bed": { "output_name": "output_bed", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput_tab": { "output_name": "output_tab", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionoutput_pdf": { "output_name": "output_pdf", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Remapped reads visualization" } } }, "workflow_outputs": [ { "output_name": "output_pdf", "uuid": "5f457235-12d7-4d76-8308-c7af651f6492", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/small_rna_maps/small_rna_maps/2.14.0", "input_connections": { "inputs": { "output_name": "output", "id": 6 } }, "inputs": [ { "name": "inputs", "description": "runtime parameter for tool small_rna_maps" } ], "position": { "top": 577, "left": 1668.5 }, "tool_state": "{\"inputs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"ylimits_cond\": \"{\\\"__current_case__\\\": 1, \\\"ylimits\\\": \\\"false\\\"}\", \"minsize\": \"\\\"18\\\"\", \"maxsize\": \"\\\"30\\\"\", \"normalization\": \"\\\"1\\\"\", \"plots_options\": \"{\\\"__current_case__\\\": 0, \\\"extra_plot\\\": \\\"Counts\\\", \\\"first_plot\\\": \\\"Size\\\", \\\"plots_options_selector\\\": \\\"two_plot\\\"}\"}", "label": "Visualize remapped reads", "type": "tool", "id": 8, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "14adf24603b6", "name": "small_rna_maps", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "small_rna_maps" } }, "annotation": "", "name": "Metavisitor: Workflow for remapping in Use Cases 1-1,2,3" }