Mercurial > repos > artbio > metavisitor_2_workflows
view Galaxy-Workflow-Metavisitor__Spades_test_in_Use_Case_2-2.ga @ 1:6396f06de8a9 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows/metavisitor_2_workflows commit 46881c948d0ad16e8c687657648402eeb5a886fb
author | artbio |
---|---|
date | Wed, 21 Aug 2019 06:30:46 -0400 |
parents | c375489bbcb0 |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "uuid": "4eeec630-2c47-43fc-a0c0-1c42f7b24bcd", "tags": [], "format-version": "0.1", "version": 2, "steps": { "1": { "tool_id": null, "errors": null, "uuid": "ba008c06-f14c-4096-8e67-aaadc5f4da7f", "tool_version": null, "outputs": [], "workflow_outputs": [ { "output_name": "output", "uuid": "bfdbc10f-dec4-4545-b356-0b85e6171b1d", "label": null } ], "annotation": "", "content_id": null, "input_connections": {}, "inputs": [], "position": { "top": 538.5, "left": 1479.5 }, "tool_state": "{}", "label": "Protein Blast database", "type": "data_input", "id": 1, "name": "Input dataset" }, "0": { "tool_id": null, "errors": null, "uuid": "c51fc830-0dbc-45e9-ac2a-11ba565237a2", "tool_version": null, "outputs": [], "workflow_outputs": [ { "output_name": "output", "uuid": "4622ab31-8367-4919-8b83-e7ec39ea1b32", "label": null } ], "annotation": "", "content_id": null, "input_connections": {}, "inputs": [], "position": { "top": 269.5, "left": 200 }, "tool_state": "{\"collection_type\": \"list\"}", "label": "Fastq read 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": "b6115894-4559-4388-8a64-4e7f909ab90c", "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": {} }, "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": [], "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_unaligned_reads_l", "id": 2 } }, "inputs": [ { "name": "global_condition", "description": "runtime parameter for tool Concatenate multiple datasets" } ], "position": { "top": 276.5, "left": 782 }, "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": null, "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/devteam/bowtie2/bowtie2/2.3.4.3", "errors": null, "uuid": "23f680f2-4891-4bea-a920-700ef1e95149", "tool_version": "2.3.4.3", "outputs": [ { "type": "fastqsanger", "name": "output_unaligned_reads_l" }, { "type": "fastqsanger", "name": "output_aligned_reads_l" }, { "type": "fastqsanger", "name": "output_aligned_reads_r" }, { "type": "fastqsanger", "name": "output_unaligned_reads_r" }, { "type": "bam", "name": "output" }, { "type": "txt", "name": "mapping_stats" } ], "post_job_actions": { "DeleteIntermediatesActionoutput_unaligned_reads_l": { "output_name": "output_unaligned_reads_l", "action_type": "DeleteIntermediatesAction", "action_arguments": {} }, "HideDatasetActionoutput_unaligned_reads_r": { "output_name": "output_unaligned_reads_r", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput": { "output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput_aligned_reads_l": { "output_name": "output_aligned_reads_l", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionmapping_stats": { "output_name": "mapping_stats", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput_aligned_reads_r": { "output_name": "output_aligned_reads_r", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput_unaligned_reads_l": { "output_name": "output_unaligned_reads_l", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [], "annotation": "Get non-host reads", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3", "input_connections": { "library|input_1": { "output_name": "output", "id": 0 } }, "inputs": [ { "name": "library", "description": "runtime parameter for tool Bowtie2" } ], "position": { "top": 302.5, "left": 477 }, "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 0, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"single\\\", \\\"unaligned_file\\\": \\\"true\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"AgamP4\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 1, \\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"effort_options\\\": {\\\"__current_case__\\\": 1, \\\"effort_options_selector\\\": \\\"no\\\"}, \\\"input_options\\\": {\\\"__current_case__\\\": 0, \\\"input_options_selector\\\": \\\"yes\\\", \\\"int_quals\\\": \\\"false\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"skip\\\": \\\"0\\\", \\\"solexa_quals\\\": \\\"false\\\", \\\"trim3\\\": \\\"20\\\", \\\"trim5\\\": \\\"0\\\"}, \\\"other_options\\\": {\\\"__current_case__\\\": 1, \\\"other_options_selector\\\": \\\"no\\\"}, \\\"reporting_options\\\": {\\\"__current_case__\\\": 1, \\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\"}, \\\"scoring_options\\\": {\\\"__current_case__\\\": 1, \\\"scoring_options_selector\\\": \\\"no\\\"}}\"}", "label": "Align to host", "type": "tool", "id": 2, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "017aba02828d", "name": "bowtie2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Bowtie2" }, "5": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", "errors": null, "uuid": "71675030-b426-4e72-ac38-3dcb5c50f420", "tool_version": "1.1", "outputs": [ { "type": "fasta", "name": "output" } ], "post_job_actions": {}, "workflow_outputs": [ { "output_name": "output", "uuid": "719383b2-64cc-4aaf-abe5-deeb362fffa3", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", "input_connections": { "input": { "output_name": "out_contigs", "id": 4 } }, "inputs": [ { "name": "input", "description": "runtime parameter for tool Filter sequences by length" } ], "position": { "top": 316.5, "left": 1482.5 }, "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"5000\\\"\"}", "label": "Get contigs >5kb", "type": "tool", "id": 5, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "2fd6033d0e9c", "name": "fasta_filter_by_length", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Filter sequences by length" }, "4": { "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1", "errors": null, "uuid": "b32de930-c74c-4836-b127-0ca17f064df5", "tool_version": "3.12.0+galaxy1", "outputs": [ { "type": "tabular", "name": "out_contig_stats" }, { "type": "tabular", "name": "out_scaffold_stats" }, { "type": "fasta", "name": "out_contigs" }, { "type": "fasta", "name": "out_scaffolds" }, { "type": "txt", "name": "out_log" }, { "type": "txt", "name": "contig_graph" }, { "type": "txt", "name": "scaffold_graph" } ], "post_job_actions": { "HideDatasetActionout_contig_stats": { "output_name": "out_contig_stats", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionout_log": { "output_name": "out_log", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionout_scaffolds": { "output_name": "out_scaffolds", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionout_contigs": { "output_name": "out_contigs", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionout_scaffold_stats": { "output_name": "out_scaffold_stats", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [ { "output_name": "scaffold_graph", "uuid": "783ef468-ee48-47dd-bcdc-a68c346935b5", "label": null }, { "output_name": "contig_graph", "uuid": "d40dcf64-77ce-45ad-b8d1-f29bfd15daf2", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1", "input_connections": { "libraries_0|files_0|file_type|unpaired_reads": { "output_name": "out_file1", "id": 3 } }, "inputs": [ { "name": "pacbio_reads", "description": "runtime parameter for tool SPAdes" }, { "name": "nanopore_reads", "description": "runtime parameter for tool SPAdes" }, { "name": "trusted_contigs", "description": "runtime parameter for tool SPAdes" }, { "name": "untrusted_contigs", "description": "runtime parameter for tool SPAdes" }, { "name": "sanger_reads", "description": "runtime parameter for tool SPAdes" } ], "position": { "top": 306.5, "left": 1093.5 }, "tool_state": "{\"pacbio_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"libraries\": \"[{\\\"__index__\\\": 0, \\\"files\\\": [{\\\"__index__\\\": 0, \\\"file_type\\\": {\\\"__current_case__\\\": 3, \\\"type\\\": \\\"unpaired\\\", \\\"unpaired_reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}], \\\"lib_type\\\": \\\"paired_end\\\", \\\"orientation\\\": \\\"fr\\\"}]\", \"iontorrent\": \"\\\"false\\\"\", \"cov\": \"{\\\"__current_case__\\\": 2, \\\"state\\\": \\\"auto\\\"}\", \"__page__\": null, \"nanopore_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"trusted_contigs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"untrusted_contigs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"kmer_choice\": \"{\\\"__current_case__\\\": 1, \\\"auto_kmer_choice\\\": \\\"true\\\"}\", \"scaffold_graph_out\": \"\\\"true\\\"\", \"onlyassembler\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"sanger_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sc\": \"\\\"false\\\"\", \"careful\": \"\\\"false\\\"\", \"contig_graph_out\": \"\\\"true\\\"\"}", "label": "Assemble contigs using SPADES", "type": "tool", "id": 4, "tool_shed_repository": { "owner": "nml", "changeset_revision": "b8d633fbf5f5", "name": "spades", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "SPAdes" }, "7": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/blastparser_and_hits/BlastParser_and_hits/2.6.1", "errors": null, "uuid": "f281973f-fc95-4393-881f-353a8709c55b", "tool_version": "2.6.1", "outputs": [ { "type": "tabular", "name": "tabularOutput" }, { "type": "fasta", "name": "fastaOutput" }, { "type": "fasta", "name": "al_sequences" }, { "type": "fasta", "name": "un_sequences" } ], "post_job_actions": { "HideDatasetActional_sequences": { "output_name": "al_sequences", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActiontabularOutput": { "output_name": "tabularOutput", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Assembled contigs matching vir2" } }, "HideDatasetActionun_sequences": { "output_name": "un_sequences", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionfastaOutput": { "output_name": "fastaOutput", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [ { "output_name": "tabularOutput", "uuid": "b99946a8-3be2-456e-ba2a-89a2fd893287", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/blastparser_and_hits/BlastParser_and_hits/2.6.1", "input_connections": { "blast": { "output_name": "output1", "id": 6 }, "sequences": { "output_name": "output", "id": 5 } }, "inputs": [ { "name": "blast", "description": "runtime parameter for tool Parse blast output and compile hits" }, { "name": "sequences", "description": "runtime parameter for tool Parse blast output and compile hits" } ], "position": { "top": 347, "left": 2136 }, "tool_state": "{\"__page__\": null, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "label": null, "type": "tool", "id": 7, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "b4c9c085d709", "name": "blastparser_and_hits", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Parse blast output and compile hits" }, "6": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1", "errors": null, "uuid": "80f46de2-9775-4658-88e2-ebe915185e2f", "tool_version": "0.3.1", "outputs": [ { "type": "tabular", "name": "output1" } ], "post_job_actions": {}, "workflow_outputs": [ { "output_name": "output1", "uuid": "37874627-1583-40e3-9d59-96c0ffa3d5c5", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1", "input_connections": { "query": { "output_name": "output", "id": 5 }, "db_opts|histdb": { "output_name": "output", "id": 1 } }, "inputs": [ { "name": "db_opts", "description": "runtime parameter for tool NCBI BLAST+ blastx" }, { "name": "query", "description": "runtime parameter for tool NCBI BLAST+ blastx" } ], "position": { "top": 460.5, "left": 1763 }, "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"__current_case__\\\": 2, \\\"ext_cols\\\": [\\\"slen\\\"], \\\"ids_cols\\\": null, \\\"misc_cols\\\": null, \\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"tax_cols\\\": null}\", \"adv_opts\": \"{\\\"__current_case__\\\": 0, \\\"adv_opts_selector\\\": \\\"basic\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\", \\\"db_opts_selector\\\": \\\"histdb\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"subject\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "label": "Blastx vs vir2", "type": "tool", "id": 6, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e25d3acf6e68", "name": "ncbi_blast_plus", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "NCBI BLAST+ blastx" } }, "annotation": "", "name": "Metavisitor: Spades test in Use Case 2-2" }