Mercurial > repos > drosofff > metavisitor_workflows
view Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.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 2-1", "steps": { "0": { "annotation": "", "content_id": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset Collection" } ], "label": null, "name": "Input dataset collection", "outputs": [], "position": { "left": 110.9375, "top": 269.37501525878906 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", "tool_version": null, "type": "data_collection_input", "uuid": "None", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "4e1d736b-a314-441c-95ef-c4e7fbde52e6" } ] }, "1": { "annotation": "", "content_id": null, "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Blast Protein database" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 1088.5938110351562, "top": 839.96533203125 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Blast Protein database\"}", "tool_version": null, "type": "data_input", "uuid": "ee9f8f76-6682-4688-88ad-8263109cf051", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "18d27e4d-ada8-48e3-b69a-ce878a19d260" } ] }, "2": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3", "id": 2, "input_connections": {}, "inputs": [], "label": null, "name": "Retrieve FASTA from NCBI", "outputs": [ { "name": "outfilename", "type": "fasta" }, { "name": "logfile", "type": "txt" } ], "position": { "left": 1736.5973052978516, "top": 1034.4966125488281 }, "post_job_actions": { "HideDatasetActionlogfile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "logfile" }, "HideDatasetActionoutfilename": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outfilename" }, "RenameDatasetActionoutfilename": { "action_arguments": { "newname": "DCV NC_001834.1 Guide" }, "action_type": "RenameDatasetAction", "output_name": "outfilename" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"NC_001834.1\\\"\", \"dbname\": \"\\\"nuccore\\\"\"}", "tool_version": "0.9.3", "type": "tool", "uuid": "None", "workflow_outputs": [] }, "3": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", "id": 3, "input_connections": { "input": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "Clip adapter", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 254.84375, "top": 419.3750247955322 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"50\\\"\", \"__rerun_remap_job_id__\": null, \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"TGGAATTCTCGGGTGCCAAG\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"Nmode\": \"\\\"accept\\\"\"}", "tool_version": "1.3.6", "type": "tool", "uuid": "None", "workflow_outputs": [] }, "4": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", "id": 4, "input_connections": { "input_file": { "id": 2, "output_name": "outfilename" } }, "inputs": [], "label": null, "name": "NCBI BLAST+ makeblastdb", "outputs": [ { "name": "outfile", "type": "data" } ], "position": { "left": 2035.6077270507812, "top": 918.4896545410156 }, "post_job_actions": { "HideDatasetActionoutfile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outfile" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"title\": \"\\\"DCV NC_001834.1\\\"\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\", \"parse_seqids\": \"\\\"False\\\"\"}", "tool_version": "0.1.06", "type": "tool", "uuid": "None", "workflow_outputs": [] }, "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", "id": 5, "input_connections": { "input": { "id": 3, "output_name": "output" } }, "inputs": [], "label": null, "name": "Concatenate multiple datasets", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 312.77783203125, "top": 621.3715667724609 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "fasta" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" }, "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "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": "None", "workflow_outputs": [] }, "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", "id": 6, "input_connections": { "switch|input": { "id": 5, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "fasta - tabular", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 482.5694580078125, "top": 420.9722480773926 }, "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": "890947a5-b6c3-4905-9659-9f4cb58ae3de", "workflow_outputs": [] }, "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", "id": 7, "input_connections": { "switch|input": { "id": 6, "output_name": "output" } }, "inputs": [], "label": null, "name": "fasta - tabular", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 729.6007080078125, "top": 374.9653015136719 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Initial Clipped sequences" }, "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": "5807c11d-856f-466a-80b3-2854a13ed901", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "0104c422-daac-45f9-b56c-2b899f4f4c6f" } ] }, "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", "id": 8, "input_connections": { "input": { "id": 7, "output_name": "output" } }, "inputs": [], "label": null, "name": "sRbowtie", "outputs": [ { "name": "output", "type": "tabular" }, { "name": "aligned", "type": "fasta" }, { "name": "unaligned", "type": "fasta" } ], "position": { "left": 722.482666015625, "top": 602.3785095214844 }, "post_job_actions": { "HideDatasetActionaligned": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "aligned" }, "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "RenameDatasetActionunaligned": { "action_arguments": { "newname": "Non A. gambiae sequences" }, "action_type": "RenameDatasetAction", "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\\\": \\\"AgamP4\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", "uuid": "None", "workflow_outputs": [ { "label": null, "output_name": "unaligned", "uuid": "e00fc25f-c655-4854-a3e3-e1f6ae204302" } ] }, "9": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", "id": 9, "input_connections": { "input": { "id": 8, "output_name": "unaligned" } }, "inputs": [], "label": null, "name": "sRbowtie", "outputs": [ { "name": "output", "type": "tabular" }, { "name": "aligned", "type": "fasta" }, { "name": "unaligned", "type": "fasta" } ], "position": { "left": 724.96533203125, "top": 780.3819885253906 }, "post_job_actions": { "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" }, "RenameDatasetActionunaligned": { "action_arguments": { "newname": "unmatched Plasmodium Berghei" }, "action_type": "RenameDatasetAction", "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\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", "uuid": "None", "workflow_outputs": [] }, "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", "id": 10, "input_connections": { "input": { "id": 9, "output_name": "unaligned" } }, "inputs": [], "label": null, "name": "sRbowtie", "outputs": [ { "name": "output", "type": "tabular" }, { "name": "aligned", "type": "fasta" }, { "name": "unaligned", "type": "fasta" } ], "position": { "left": 725.920166015625, "top": 996.3889465332031 }, "post_job_actions": { "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" }, "RenameDatasetActionunaligned": { "action_arguments": { "newname": "Unaligned PhiX174" }, "action_type": "RenameDatasetAction", "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\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", "uuid": "None", "workflow_outputs": [] }, "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", "id": 11, "input_connections": { "inputs_0|input": { "id": 10, "output_name": "unaligned" } }, "inputs": [], "label": null, "name": "Oases_optimiser", "outputs": [ { "name": "transcripts", "type": "fasta" } ], "position": { "left": 1090.4688110351562, "top": 339.39238357543945 }, "post_job_actions": { "RenameDatasetActiontranscripts": { "action_arguments": { "newname": "Oases 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\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", "tool_version": "1.1.4", "type": "tool", "uuid": "None", "workflow_outputs": [ { "label": null, "output_name": "transcripts", "uuid": "68909f85-3532-47e2-956b-73dfad6bdc5f" } ] }, "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", "id": 12, "input_connections": { "db_opts|histdb": { "id": 1, "output_name": "output" }, "query": { "id": 11, "output_name": "transcripts" } }, "inputs": [], "label": null, "name": "NCBI BLAST+ blastx", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 1149.49658203125, "top": 607.3785095214844 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"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\\\"]}\"}", "tool_version": "0.1.06", "type": "tool", "uuid": "None", "workflow_outputs": [ { "label": null, "output_name": "output1", "uuid": "2bcd52a4-3023-4f30-918d-0383c0ef4455" } ] }, "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", "id": 13, "input_connections": { "blast": { "id": 12, "output_name": "output1" }, "sequences": { "id": 11, "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": 1454.5486907958984, "top": 436.9097480773926 }, "post_job_actions": { "HideDatasetActional_sequences": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "al_sequences" }, "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\": \"{\\\"use_filters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", "tool_version": "2.4.3", "type": "tool", "uuid": "32401021-0c03-4c16-a8a3-b08c54d34ce5", "workflow_outputs": [ { "label": null, "output_name": "tabularOutput", "uuid": "0ecb04ea-b8fe-45ce-aa11-c4a67f1e17dd" }, { "label": null, "output_name": "fastaOutput", "uuid": "f37bfebc-7b87-4dfc-a98c-2cdc3b18a84a" } ] }, "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", "id": 14, "input_connections": { "input": { "id": 13, "output_name": "fastaOutput" } }, "inputs": [], "label": null, "name": "Pick Fasta sequences", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 1746.0938415527344, "top": 672.5000305175781 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"query\": \"\\\"Drosophila_C_virus\\\"\"}", "tool_version": "0.9.0", "type": "tool", "uuid": "None", "workflow_outputs": [] }, "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", "id": 15, "input_connections": { "input": { "id": 13, "output_name": "fastaOutput" } }, "inputs": [], "label": null, "name": "Pick Fasta sequences", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 1745.104248046875, "top": 765.4861450195312 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"query\": \"\\\"Cricket_paralysis_virus\\\"\"}", "tool_version": "0.9.0", "type": "tool", "uuid": "None", "workflow_outputs": [] }, "16": { "annotation": "", "content_id": "cat1", "id": 16, "input_connections": { "input1": { "id": 14, "output_name": "output" }, "queries_0|input2": { "id": 15, "output_name": "output" } }, "inputs": [], "label": null, "name": "Concatenate datasets", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1983.5938415527344, "top": 680.4861450195312 }, "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Dicistroviridae Hits" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "cat1", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", "tool_version": "1.0.0", "type": "tool", "uuid": "None", "workflow_outputs": [ { "label": null, "output_name": "out_file1", "uuid": "f73ab6cc-279f-4a9e-8860-73e3b206b9ca" } ] }, "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0", "id": 17, "input_connections": { "inputSequences": { "id": 16, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "cap3", "outputs": [ { "name": "contigsandsinglets", "type": "fasta" }, { "name": "cap3stdout", "type": "txt" }, { "name": "contigs", "type": "fasta" }, { "name": "contigsqual", "type": "txt" }, { "name": "contigslink", "type": "txt" }, { "name": "ace", "type": "txt" }, { "name": "info", "type": "txt" }, { "name": "singlets", "type": "txt" } ], "position": { "left": 2192.100830078125, "top": 513.489616394043 }, "post_job_actions": { "HideDatasetActionace": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "ace" }, "HideDatasetActioncap3stdout": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "cap3stdout" }, "HideDatasetActioncontigs": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "contigs" }, "HideDatasetActioncontigslink": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "contigslink" }, "HideDatasetActioncontigsqual": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "contigsqual" }, "HideDatasetActioninfo": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "info" }, "HideDatasetActionsinglets": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "singlets" }, "RenameDatasetActioncontigs": { "action_arguments": { "newname": "CAP assemblies of Dicistroviridae hits" }, "action_type": "RenameDatasetAction", "output_name": "contigs" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0", "tool_state": "{\"overlapidentity\": \"\\\"90\\\"\", \"inputSequences\": \"null\", \"__rerun_remap_job_id__\": null, \"overlaplength\": \"\\\"40\\\"\", \"__page__\": 0}", "tool_version": "1.2.0", "type": "tool", "uuid": "None", "workflow_outputs": [ { "label": null, "output_name": "contigsandsinglets", "uuid": "e413fdea-3b18-40c1-b423-cf2bd33eeadf" } ] }, "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.06", "id": 18, "input_connections": { "db_opts|histdb": { "id": 4, "output_name": "outfile" }, "query": { "id": 17, "output_name": "contigsandsinglets" } }, "inputs": [], "label": null, "name": "NCBI BLAST+ tblastx", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 2424.0973510742188, "top": 837.5000305175781 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.06", "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"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": "0.1.06", "type": "tool", "uuid": "None", "workflow_outputs": [ { "label": null, "output_name": "output1", "uuid": "7ad377ba-ad8f-421f-af4c-6835a1994f46" } ] }, "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", "id": 19, "input_connections": { "blast_tab": { "id": 18, "output_name": "output1" }, "guideSequence": { "id": 2, "output_name": "outfilename" }, "sequences": { "id": 17, "output_name": "contigsandsinglets" } }, "inputs": [], "label": null, "name": "blast_to_scaffold", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 2718.003662109375, "top": 597.9167022705078 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "New AnCV sequences in DCV scaffold" }, "action_type": "RenameDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", "tool_state": "{\"__page__\": 0, \"guideSequence\": \"null\", \"blast_tab\": \"null\", \"__rerun_remap_job_id__\": null, \"sequences\": \"null\"}", "tool_version": "0.9.0", "type": "tool", "uuid": "d6fcfcf9-1b9b-4ac3-8217-f7ddbc84be91", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "c052be17-d78e-4a17-891c-7154936c7935" } ] } }, "uuid": "ac35209c-d243-403c-95c7-5500b022ae10" }