Mercurial > repos > drosofff > metavisitor_workflows
view Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-1.ga @ 0:4a47903bb4df draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
author | drosofff |
---|---|
date | Tue, 05 Apr 2016 06:42:47 -0400 |
parents | |
children | 48b020a0d2f7 |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Metavisitor: Workflow for Use Case 3-1", "steps": { "0": { "annotation": "", "content_id": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Fever Patient Sequences collection" } ], "label": null, "name": "Input dataset collection", "outputs": [], "position": { "left": 207.96875, "top": 199.90625 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"collection_type\": \"list\", \"name\": \"Fever Patient Sequences collection\"}", "tool_version": null, "type": "data_collection_input", "uuid": "21bdc466-e175-4b9c-aacc-9ba72a877535", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "0abd6e13-fa30-4dd4-ad60-90b7fef1a8bf" } ] }, "1": { "annotation": "", "content_id": null, "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Nucleotide Viral Blast Database" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 876.109375, "top": 1158.046875 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Nucleotide Viral Blast Database\"}", "tool_version": null, "type": "data_input", "uuid": "8a789998-8ad6-495f-b923-d7bfd02896f4", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "05aef397-b0f5-4556-adb5-be963df7d67f" } ] }, "2": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", "id": 2, "input_connections": { "input": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "FASTQ to FASTA", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 256.5625, "top": 327.625 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", "tool_state": "{\"input\": \"null\", \"RENAMESEQ\": \"\\\"-r\\\"\", \"SKIPN\": \"\\\"-n\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0.0", "type": "tool", "uuid": "c7160a54-8152-41b9-870e-89ecbcbcb7dc", "workflow_outputs": [] }, "3": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0", "id": 3, "input_connections": { "input": { "id": 2, "output_name": "output" } }, "inputs": [], "label": null, "name": "Trim sequences", "outputs": [ { "name": "output", "type": "input" } ], "position": { "left": 356.671875, "top": 500.65625 }, "post_job_actions": { "ChangeDatatypeActionoutput": { "action_arguments": { "newtype": "fasta" }, "action_type": "ChangeDatatypeAction", "output_name": "output" }, "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0", "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"last\": \"\\\"27\\\"\", \"first\": \"\\\"1\\\"\"}", "tool_version": "1.0.0", "type": "tool", "uuid": "5c3a9936-166d-4cf8-9df2-db679c306d4f", "workflow_outputs": [] }, "4": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", "id": 4, "input_connections": { "switch|input": { "id": 3, "output_name": "output" } }, "inputs": [], "label": null, "name": "fasta - tabular", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 536.46875, "top": 332.515625 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"fasta2tabular\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "7c179cc4-e0a4-4e8a-be6f-c445d70c721e", "workflow_outputs": [] }, "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", "id": 5, "input_connections": { "switch|input": { "id": 4, "output_name": "output" } }, "inputs": [], "label": null, "name": "fasta - tabular", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 773.484375, "top": 283.515625 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "reduced input dataset" }, "action_type": "RenameDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"tabular2fastaweight\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "f73e38bc-8998-4e77-9d4e-77c8748f3a71", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "2bee83a0-f312-474a-be28-8c90f7313f9f" } ] }, "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", "id": 6, "input_connections": { "input": { "id": 5, "output_name": "output" } }, "inputs": [], "label": null, "name": "sRbowtie", "outputs": [ { "name": "output", "type": "tabular" }, { "name": "aligned", "type": "fasta" }, { "name": "unaligned", "type": "fasta" } ], "position": { "left": 772.625, "top": 461.625 }, "post_job_actions": { "DeleteIntermediatesActionoutput": { "action_arguments": {}, "action_type": "DeleteIntermediatesAction", "output_name": "output" }, "HideDatasetActionaligned": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "aligned" }, "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "HideDatasetActionunaligned": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "unaligned" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", "uuid": "41108f94-dbf9-4cbe-8bd4-acdc16c9c06c", "workflow_outputs": [] }, "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", "id": 7, "input_connections": { "input": { "id": 6, "output_name": "unaligned" } }, "inputs": [], "label": null, "name": "sRbowtie", "outputs": [ { "name": "output", "type": "tabular" }, { "name": "aligned", "type": "fasta" }, { "name": "unaligned", "type": "fasta" } ], "position": { "left": 933.671875, "top": 691.625 }, "post_job_actions": { "DeleteIntermediatesActionoutput": { "action_arguments": {}, "action_type": "DeleteIntermediatesAction", "output_name": "output" }, "HideDatasetActionaligned": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "aligned" }, "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "HideDatasetActionunaligned": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "unaligned" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"al\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"vir1\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", "uuid": "3d252e09-bbcc-45d3-9878-32e4fd8a43e5", "workflow_outputs": [] }, "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", "id": 8, "input_connections": { "inputs_0|input": { "id": 7, "output_name": "aligned" } }, "inputs": [], "label": null, "name": "Oases_optimiser", "outputs": [ { "name": "transcripts", "type": "fasta" } ], "position": { "left": 1302.109375, "top": 849.03125 }, "post_job_actions": { "RenameDatasetActiontranscripts": { "action_arguments": { "newname": "Oases viral contigs" }, "action_type": "RenameDatasetAction", "output_name": "transcripts" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"27\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"11\\\"\"}", "tool_version": "1.1.4", "type": "tool", "uuid": "b73a2fa1-bf72-4ad3-b82c-e342a21a5275", "workflow_outputs": [ { "label": null, "output_name": "transcripts", "uuid": "3395237c-c08b-4623-9172-15b52e82034c" } ] }, "9": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07", "id": 9, "input_connections": { "db_opts|histdb": { "id": 1, "output_name": "output" }, "query": { "id": 8, "output_name": "transcripts" } }, "inputs": [], "label": null, "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 1442.09375, "top": 1084.03125 }, "post_job_actions": { "RenameDatasetActionoutput1": { "action_arguments": { "newname": "blastN of oases contigs" }, "action_type": "RenameDatasetAction", "output_name": "output1" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07", "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"blastn\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"query\": \"null\"}", "tool_version": "0.1.07", "type": "tool", "uuid": "0e8b01bc-d919-4bc4-ba28-c2fde37de6b6", "workflow_outputs": [ { "label": null, "output_name": "output1", "uuid": "e24552f8-47ea-44fa-b339-254d7902e2aa" } ] }, "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", "id": 10, "input_connections": { "blast": { "id": 9, "output_name": "output1" }, "sequences": { "id": 8, "output_name": "transcripts" } }, "inputs": [], "label": null, "name": "Parse blast output and compile hits", "outputs": [ { "name": "tabularOutput", "type": "tabular" }, { "name": "fastaOutput", "type": "fasta" }, { "name": "al_sequences", "type": "fasta" }, { "name": "un_sequences", "type": "fasta" } ], "position": { "left": 1837.1875, "top": 854.625 }, "post_job_actions": { "DeleteIntermediatesActiontabularOutput": { "action_arguments": {}, "action_type": "DeleteIntermediatesAction", "output_name": "tabularOutput" }, "HideDatasetActional_sequences": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "al_sequences" }, "HideDatasetActionfastaOutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "fastaOutput" }, "HideDatasetActionun_sequences": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "un_sequences" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"filter_term_out\\\": \\\"Patent\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"0.0\\\", \\\"use_filters\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"filter_term_in\\\": \\\"\\\", \\\"filter_maxScore\\\": \\\"0.0\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", "tool_version": "2.4.3", "type": "tool", "uuid": "4acd0e30-b867-43e3-99e9-88d0c602c8f3", "workflow_outputs": [ { "label": null, "output_name": "tabularOutput", "uuid": "2ee6f85d-cc71-4ed1-8a40-16e98ff3d27a" } ] }, "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", "id": 11, "input_connections": { "input": { "id": 10, "output_name": "tabularOutput" } }, "inputs": [], "label": null, "name": "Concatenate multiple datasets", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 2180.5, "top": 1016.5 }, "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Virus identification by patient" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "0.2", "type": "tool", "uuid": "b4a09441-4f8f-46ec-81ff-c2a87928d1d6", "workflow_outputs": [ { "label": null, "output_name": "out_file1", "uuid": "12afc0c5-36d1-4876-bd60-3b61e5c278f6" } ] } }, "uuid": "2757d825-19dc-4e6d-964d-724eef88b5b7" }