Mercurial > repos > artbio > metavisitor_2_workflows
view Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.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": "1187ab6d-a4f6-4ee7-817c-d12db902fed7", "tags": [], "format-version": "0.1", "version": 3, "steps": { "11": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/2.0.0", "errors": null, "uuid": "bd3f2dd0-b170-433d-b1e8-2b0f303006a7", "tool_version": "2.0.0", "outputs": [ { "type": "fasta", "name": "contigsandsinglets" }, { "type": "txt", "name": "cap3stdout" }, { "type": "fasta", "name": "contigs" }, { "type": "txt", "name": "contigsqual" }, { "type": "txt", "name": "contigslink" }, { "type": "txt", "name": "ace" }, { "type": "txt", "name": "info" }, { "type": "txt", "name": "singlets" } ], "post_job_actions": { "HideDatasetActioninfo": { "output_name": "info", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActioncontigsqual": { "output_name": "contigsqual", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActioncontigsandsinglets": { "output_name": "contigsandsinglets", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "CAP3 assembled contigs" } }, "HideDatasetActioncontigslink": { "output_name": "contigslink", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActioncontigs": { "output_name": "contigs", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActioncap3stdout": { "output_name": "cap3stdout", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionsinglets": { "output_name": "singlets", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionace": { "output_name": "ace", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [ { "output_name": "contigsandsinglets", "uuid": "e2dff9ee-9235-4087-9a51-30b5b9974537", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/2.0.0", "input_connections": { "inputSequences": { "output_name": "fastaOutput", "id": 10 } }, "inputs": [ { "name": "inputSequences", "description": "runtime parameter for tool cap3" } ], "position": { "top": 633, "left": 2061.5 }, "tool_state": "{\"overlapidentity\": \"\\\"90\\\"\", \"inputSequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"overlaplength\": \"\\\"40\\\"\", \"__page__\": null}", "label": "CAP3 to re-assembe contigs", "type": "tool", "id": 11, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "d76a0d8a9eac", "name": "cap3", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "cap3" }, "10": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/blastparser_and_hits/BlastParser_and_hits/2.6.1", "errors": null, "uuid": "bac749b9-96e4-4a92-baac-cd160c09f9ec", "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": { "RenameDatasetActionfastaOutput": { "output_name": "fastaOutput", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Assembled contigs hitting viral database" } }, "HideDatasetActional_sequences": { "output_name": "al_sequences", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionun_sequences": { "output_name": "un_sequences", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [ { "output_name": "tabularOutput", "uuid": "f858a698-d9dd-4cc2-a047-6664b0519271", "label": null }, { "output_name": "fastaOutput", "uuid": "d9c341c8-d826-4633-a6a5-9462677092d8", "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": 9 }, "sequences": { "output_name": "transcripts", "id": 8 } }, "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": 404, "left": 1740 }, "tool_state": "{\"__page__\": null, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 1, \\\"filter_maxScore\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"0.0\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_term_in\\\": \\\"Nora_virus\\\", \\\"filter_term_out\\\": \\\"JX220408.1\\\", \\\"use_filters\\\": \\\"yes\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "label": "Get viral contigs", "type": "tool", "id": 10, "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" }, "13": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/blast_to_scaffold/blast2scaffold/1.0.0", "errors": null, "uuid": "7f0913f8-f7f9-4ba3-878c-9c502460331d", "tool_version": "1.0.0", "outputs": [ { "type": "fasta", "name": "output" } ], "post_job_actions": { "HideDatasetActionoutput": { "output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionoutput": { "output_name": "output", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "generated CDS" } } }, "workflow_outputs": [], "annotation": "Generate CDS from aligned contigs", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/blast_to_scaffold/blast2scaffold/1.0.0", "input_connections": { "guideSequence": { "output_name": "outfile", "id": 2 }, "blast_tab": { "output_name": "output1", "id": 12 }, "sequences": { "output_name": "contigsandsinglets", "id": 11 } }, "inputs": [ { "name": "guideSequence", "description": "runtime parameter for tool blast_to_scaffold" }, { "name": "blast_tab", "description": "runtime parameter for tool blast_to_scaffold" }, { "name": "sequences", "description": "runtime parameter for tool blast_to_scaffold" } ], "position": { "top": 669, "left": 2728.5 }, "tool_state": "{\"__page__\": null, \"guideSequence\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast_tab\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "label": "Generate CDS", "type": "tool", "id": 13, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "7d96b28eec49", "name": "blast_to_scaffold", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "blast_to_scaffold" }, "12": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1", "errors": null, "uuid": "4f996123-d155-426a-ba26-e649c422431e", "tool_version": "0.3.1", "outputs": [ { "type": "tabular", "name": "output1" } ], "post_job_actions": { "HideDatasetActionoutput1": { "output_name": "output1", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionoutput1": { "output_name": "output1", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Contigs aligned to ${ncbi_guide_ID}" } } }, "workflow_outputs": [], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1", "input_connections": { "query": { "output_name": "contigsandsinglets", "id": 11 }, "db_opts|histdb": { "output_name": "outfile", "id": 4 } }, "inputs": [ { "name": "db_opts", "description": "runtime parameter for tool NCBI BLAST+ blastn" }, { "name": "query", "description": "runtime parameter for tool NCBI BLAST+ blastn" } ], "position": { "top": 837, "left": 2402 }, "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\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "label": "Blast contigs to specific virus database", "type": "tool", "id": 12, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e25d3acf6e68", "name": "ncbi_blast_plus", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "NCBI BLAST+ blastn" }, "14": { "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0", "errors": null, "uuid": "c81173fb-317d-4c00-9da8-f0072b62a569", "tool_version": "1.0.0", "outputs": [ { "type": "input", "name": "out_file1" } ], "post_job_actions": { "ChangeDatatypeActionout_file1": { "output_name": "out_file1", "action_type": "ChangeDatatypeAction", "action_arguments": { "newtype": "fasta" } }, "RenameDatasetActionout_file1": { "output_name": "out_file1", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Nora_MV_${ncbi_guide_ID}_guided" } } }, "workflow_outputs": [ { "output_name": "out_file1", "uuid": "e202eeb0-f65c-4295-afe0-44a56634a452", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0", "input_connections": { "input": { "output_name": "output", "id": 13 } }, "inputs": [ { "name": "input", "description": "runtime parameter for tool Regex Find And Replace" } ], "position": { "top": 927, "left": 2971 }, "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"pattern\\\": \\\">.+\\\", \\\"replacement\\\": \\\">Nora_MV\\\"}]\", \"__page__\": null}", "label": "Change CDS header", "type": "tool", "id": 14, "tool_shed_repository": { "owner": "galaxyp", "changeset_revision": "209b7c5ee9d7", "name": "regex_find_replace", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Regex Find And Replace" }, "1": { "tool_id": null, "errors": null, "uuid": "462eb78f-9844-42d6-8087-19f2e1e801ca", "tool_version": null, "outputs": [], "workflow_outputs": [ { "output_name": "output", "uuid": "6bd2d24e-e12f-41fe-9308-631cc6718143", "label": null } ], "annotation": "", "content_id": null, "input_connections": {}, "inputs": [], "position": { "top": 976.9833374023438, "left": 1205.9666748046875 }, "tool_state": "{}", "label": "viral nucleotide BLAST database (V2)", "type": "data_input", "id": 1, "name": "Input dataset" }, "0": { "tool_id": null, "errors": null, "uuid": "aa5c2a9c-0f52-4884-9f1c-74432b24af61", "tool_version": null, "outputs": [], "workflow_outputs": [ { "output_name": "output", "uuid": "b5da90b2-1c4f-4646-8c70-fc9952f6cb94", "label": null } ], "annotation": "", "content_id": null, "input_connections": {}, "inputs": [], "position": { "top": 163, "left": 200 }, "tool_state": "{\"collection_type\": \"list\"}", "label": "Fastq files", "type": "data_collection_input", "id": 0, "name": "Input dataset collection" }, "3": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/yac_clipper/yac/2.3.0", "errors": null, "uuid": "41212793-f400-4bd6-9827-c083025f3e01", "tool_version": "2.3.0", "outputs": [ { "type": "input", "name": "output" } ], "post_job_actions": { "RenameDatasetActionoutput": { "output_name": "output", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "#{input} clipped" } } }, "workflow_outputs": [ { "output_name": "output", "uuid": "3939be31-c091-4dbe-86a7-fd05c01f9598", "label": null } ], "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": 318, "left": 364.5 }, "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": 3, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "f7947c5a18b8", "name": "yac_clipper", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Clip adapter" }, "2": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0", "errors": null, "uuid": "13214523-9fb0-4e23-8cdf-f389331ba0c9", "tool_version": "2.3.0", "outputs": [ { "type": "fasta", "name": "outfile" }, { "type": "txt", "name": "logfile" } ], "post_job_actions": { "HideDatasetActionlogfile": { "output_name": "logfile", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionoutfile": { "output_name": "outfile", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "${ncbi_guide_ID}" } } }, "workflow_outputs": [ { "output_name": "outfile", "uuid": "9c9b23f2-66ae-4eeb-88f1-e4a0a8bd596b", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0", "input_connections": {}, "inputs": [], "position": { "top": 1043, "left": 1750 }, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"${ncbi_guide_ID}\\\"\", \"dbname\": \"\\\"nuccore\\\"\", \"dry_run\": \"\\\"false\\\"\"}", "label": null, "type": "tool", "id": 2, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "c667d0ee39f5", "name": "fetch_fasta_from_ncbi", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Retrieve FASTA from NCBI" }, "5": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", "errors": null, "uuid": "02a6f0a8-8f83-4b0f-85ad-0370a5753a13", "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} concatenated" } }, "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", "id": 3 } }, "inputs": [ { "name": "global_condition", "description": "runtime parameter for tool Concatenate multiple datasets" } ], "position": { "top": 492.5, "left": 474 }, "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": 5, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "55cf9d9defd1", "name": "concatenate_multiple_datasets", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Concatenate multiple datasets" }, "4": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1", "errors": null, "uuid": "1a39e6e8-8079-4f7a-b4c2-2028e5dbc2dd", "tool_version": "0.3.1", "outputs": [ { "type": "data", "name": "outfile" } ], "post_job_actions": { "HideDatasetActionoutfile": { "output_name": "outfile", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionoutfile": { "output_name": "outfile", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "#{input_file} blast database" } } }, "workflow_outputs": [], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1", "input_connections": { "input_file": { "output_name": "outfile", "id": 2 } }, "inputs": [ { "name": "mask_data_file", "description": "runtime parameter for tool NCBI BLAST+ makeblastdb" }, { "name": "input_file", "description": "runtime parameter for tool NCBI BLAST+ makeblastdb" } ], "position": { "top": 1060, "left": 2100.5 }, "tool_state": "{\"__page__\": null, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"title\": \"\\\"Blastn candidate database\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}", "label": "Make a blast database", "type": "tool", "id": 4, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e25d3acf6e68", "name": "ncbi_blast_plus", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "NCBI BLAST+ makeblastdb" }, "7": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", "errors": null, "uuid": "62876927-ee09-4764-95eb-d86548fdce73", "tool_version": "2.1.1", "outputs": [ { "type": "tabular", "name": "output" }, { "type": "input", "name": "aligned" }, { "type": "input", "name": "unaligned" } ], "post_job_actions": { "HideDatasetActionaligned": { "output_name": "aligned", "action_type": "HideDatasetAction", "action_arguments": {} }, "HideDatasetActionoutput": { "output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {} }, "RenameDatasetActionunaligned": { "output_name": "unaligned", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Non D. melanogaster sequences" } } }, "workflow_outputs": [ { "output_name": "unaligned", "uuid": "608ff661-018b-44c2-b020-59b31c5ff2d4", "label": null } ], "annotation": "Align reads to host (dm6) genome.\nThe unaligned reads will most likely have a viral source.", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", "input_connections": { "input": { "output_name": "output", "id": 6 } }, "inputs": [ { "name": "input", "description": "runtime parameter for tool sR_bowtie" } ], "position": { "top": 238, "left": 952 }, "tool_state": "{\"__page__\": null, \"output_format\": \"\\\"tabular\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 0, \\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\"}\", \"method\": \"\\\"k_option\\\"\"}", "label": "Get non-host sequences", "type": "tool", "id": 7, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "0281bb245635", "name": "sr_bowtie", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "sR_bowtie" }, "6": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/sequence_format_converter/sequence_format_converter/2.1.1", "errors": null, "uuid": "e693b793-ae94-42c8-9f59-4b4b847aa4b1", "tool_version": "2.1.1", "outputs": [ { "type": "fasta", "name": "output" } ], "post_job_actions": { "RenameDatasetActionoutput": { "output_name": "output", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Initial Clipped sequences" } } }, "workflow_outputs": [ { "output_name": "output", "uuid": "b81a3224-0d3e-4dec-996f-5fa3d525cabd", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/sequence_format_converter/sequence_format_converter/2.1.1", "input_connections": { "input": { "output_name": "out_file1", "id": 5 } }, "inputs": [ { "name": "input", "description": "runtime parameter for tool sequence_format_converter" } ], "position": { "top": 621, "left": 787.5 }, "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"output_format\": \"\\\"fastaw\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", "label": "Change sequence format to weighted fasta", "type": "tool", "id": 6, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "f1d59113125a", "name": "sequence_format_converter", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "sequence_format_converter" }, "9": { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1", "errors": null, "uuid": "37904c73-85c7-40e8-b1d5-e5f3d6a12135", "tool_version": "0.3.1", "outputs": [ { "type": "tabular", "name": "output1" } ], "post_job_actions": { "HideDatasetActionoutput1": { "output_name": "output1", "action_type": "HideDatasetAction", "action_arguments": {} } }, "workflow_outputs": [], "annotation": "Align the assembled transcripts to the viral database to filter out non-viral sequences.", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1", "input_connections": { "query": { "output_name": "transcripts", "id": 8 }, "db_opts|histdb": { "output_name": "output", "id": 1 } }, "inputs": [ { "name": "db_opts", "description": "runtime parameter for tool NCBI BLAST+ blastn" }, { "name": "query", "description": "runtime parameter for tool NCBI BLAST+ blastn" } ], "position": { "top": 690, "left": 1455 }, "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__\\\": 1, \\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"filter_query\\\": \\\"true\\\", \\\"gapextend\\\": \\\"\\\", \\\"gapopen\\\": \\\"\\\", \\\"identity_cutoff\\\": \\\"0.0\\\", \\\"max_hits\\\": \\\"5\\\", \\\"max_hsps\\\": \\\"\\\", \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"ungapped\\\": \\\"false\\\", \\\"window_size\\\": \\\"\\\", \\\"word_size\\\": \\\"\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\", \\\"db_opts_selector\\\": \\\"histdb\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"subject\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "label": "BLASTn contigs to the viral database", "type": "tool", "id": 9, "tool_shed_repository": { "owner": "devteam", "changeset_revision": "e25d3acf6e68", "name": "ncbi_blast_plus", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "NCBI BLAST+ blastn" }, "8": { "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/oases/oasesoptimiserv/1.2.2", "errors": null, "uuid": "04b99c48-2bf7-4842-b28e-c9085ffe40e9", "tool_version": "1.2.2", "outputs": [ { "type": "fasta", "name": "transcripts" } ], "post_job_actions": { "ChangeDatatypeActiontranscripts": { "output_name": "transcripts", "action_type": "ChangeDatatypeAction", "action_arguments": { "newtype": "fasta" } }, "RenameDatasetActiontranscripts": { "output_name": "transcripts", "action_type": "RenameDatasetAction", "action_arguments": { "newname": "Oases Contigs" } } }, "workflow_outputs": [ { "output_name": "transcripts", "uuid": "704bb7a9-199c-4028-a482-ebc60ab1d02e", "label": null } ], "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/oases/oasesoptimiserv/1.2.2", "input_connections": { "inputs_0|input": { "output_name": "unaligned", "id": 7 } }, "inputs": [], "position": { "top": 442, "left": 1287 }, "tool_state": "{\"__page__\": null, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", "label": "Assemble contigs", "type": "tool", "id": 8, "tool_shed_repository": { "owner": "artbio", "changeset_revision": "f7dd852c8f4c", "name": "oases", "tool_shed": "toolshed.g2.bx.psu.edu" }, "name": "Oases_optimiser" } }, "annotation": "", "name": "Metavisitor: Workflow for Use Case 1-1" }