Created
November 30, 2020 10:26
-
-
Save pvanheus/0d02e29cca7f473e0f5b9b3f7d949a86 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
{ | |
"a_galaxy_workflow": "true", | |
"annotation": "", | |
"format-version": "0.1", | |
"name": "TB phylogeny - enhanced from 0.1.3", | |
"steps": { | |
"0": { | |
"annotation": "Reference genome FASTA", | |
"content_id": null, | |
"errors": null, | |
"id": 0, | |
"input_connections": {}, | |
"inputs": [ | |
{ | |
"description": "Reference genome FASTA", | |
"name": "reference" | |
} | |
], | |
"label": "reference", | |
"name": "Input dataset", | |
"outputs": [], | |
"position": { | |
"bottom": 564.7166748046875, | |
"height": 61.79998779296875, | |
"left": -469, | |
"right": -269, | |
"top": 502.91668701171875, | |
"width": 200, | |
"x": -469, | |
"y": 502.91668701171875 | |
}, | |
"tool_id": null, | |
"tool_state": "{\"optional\": false}", | |
"tool_version": null, | |
"type": "data_input", | |
"uuid": "5ae6ff5d-cebe-4554-ba4e-3378e622aa85", | |
"workflow_outputs": [ | |
{ | |
"label": null, | |
"output_name": "output", | |
"uuid": "442e01b1-b784-4b27-a79c-eacbfe76cdee" | |
} | |
] | |
}, | |
"1": { | |
"annotation": "List of Paired-end Sequence Reads", | |
"content_id": null, | |
"errors": null, | |
"id": 1, | |
"input_connections": {}, | |
"inputs": [ | |
{ | |
"description": "List of Paired-end Sequence Reads", | |
"name": "sequence_reads_list_paired" | |
} | |
], | |
"label": "sequence_reads_list_paired", | |
"name": "Input dataset collection", | |
"outputs": [], | |
"position": { | |
"bottom": 675.1166839599609, | |
"height": 82.19999694824219, | |
"left": -469, | |
"right": -269, | |
"top": 592.9166870117188, | |
"width": 200, | |
"x": -469, | |
"y": 592.9166870117188 | |
}, | |
"tool_id": null, | |
"tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}", | |
"tool_version": null, | |
"type": "data_collection_input", | |
"uuid": "74066928-fcd0-40b6-be2e-3ccf62b9ecd5", | |
"workflow_outputs": [ | |
{ | |
"label": null, | |
"output_name": "output", | |
"uuid": "24de2866-5e44-4183-afe1-e81bae0e9c61" | |
} | |
] | |
}, | |
"2": { | |
"annotation": "", | |
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1", | |
"errors": null, | |
"id": 2, | |
"input_connections": { | |
"single_paired|paired_input": { | |
"id": 1, | |
"output_name": "output" | |
} | |
}, | |
"inputs": [], | |
"label": null, | |
"name": "fastp", | |
"outputs": [ | |
{ | |
"name": "output_paired_coll", | |
"type": "input" | |
}, | |
{ | |
"name": "report_html", | |
"type": "html" | |
} | |
], | |
"position": { | |
"bottom": 667.3166809082031, | |
"height": 164.39999389648438, | |
"left": -183, | |
"right": 17, | |
"top": 502.91668701171875, | |
"width": 200, | |
"x": -183, | |
"y": 502.91668701171875 | |
}, | |
"post_job_actions": { | |
"HideDatasetActionoutput_paired_coll": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "output_paired_coll" | |
}, | |
"HideDatasetActionreport_html": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "report_html" | |
} | |
}, | |
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1", | |
"tool_shed_repository": { | |
"changeset_revision": "1d8fe9bc4cb0", | |
"name": "fastp", | |
"owner": "iuc", | |
"tool_shed": "toolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": \"false\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\", \"n_base_limit\": \"\"}, \"length_filtering_options\": {\"disable_length_filtering\": \"false\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": \"false\", \"complexity_threshold\": \"\"}}, \"output_options\": {\"report_html\": \"true\", \"report_json\": \"false\"}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": \"false\", \"overrepresentation_sampling\": \"\"}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": \"\"}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": \"false\", \"umi_loc\": \"\", \"umi_len\": \"\", \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": \"false\", \"cut_by_quality3\": \"false\", \"cut_window_size\": \"\", \"cut_mean_quality\": \"\"}, \"base_correction_options\": {\"correction\": \"false\"}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": \"false\", \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\", \"trim_front2\": \"\", \"trim_tail2\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "0.19.5+galaxy1", | |
"type": "tool", | |
"uuid": "75798230-1656-4572-900a-c72e6b8477d0", | |
"workflow_outputs": [] | |
}, | |
"3": { | |
"annotation": "", | |
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0", | |
"errors": null, | |
"id": 3, | |
"input_connections": { | |
"fastq_input|fastq_input": { | |
"id": 2, | |
"output_name": "output_paired_coll" | |
}, | |
"reference_source|ref_file": { | |
"id": 0, | |
"output_name": "output" | |
} | |
}, | |
"inputs": [], | |
"label": "snippy", | |
"name": "snippy", | |
"outputs": [ | |
{ | |
"name": "snpvcf", | |
"type": "vcf" | |
}, | |
{ | |
"name": "snpgff", | |
"type": "gff3" | |
}, | |
{ | |
"name": "snptab", | |
"type": "tabular" | |
}, | |
{ | |
"name": "snpsum", | |
"type": "tabular" | |
}, | |
{ | |
"name": "snplog", | |
"type": "txt" | |
}, | |
{ | |
"name": "snpalign", | |
"type": "fasta" | |
}, | |
{ | |
"name": "snpconsensus", | |
"type": "fasta" | |
} | |
], | |
"position": { | |
"bottom": 1074.11669921875, | |
"height": 571.2000122070312, | |
"left": 103, | |
"right": 303, | |
"top": 502.91668701171875, | |
"width": 200, | |
"x": 103, | |
"y": 502.91668701171875 | |
}, | |
"post_job_actions": { | |
"HideDatasetActionsnpalign": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "snpalign" | |
}, | |
"HideDatasetActionsnpconsensus": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "snpconsensus" | |
}, | |
"HideDatasetActionsnpgff": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "snpgff" | |
}, | |
"HideDatasetActionsnplog": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "snplog" | |
}, | |
"HideDatasetActionsnpsum": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "snpsum" | |
}, | |
"HideDatasetActionsnptab": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "snptab" | |
}, | |
"HideDatasetActionsnpvcf": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "snpvcf" | |
}, | |
"RenameDatasetActionsnpvcf": { | |
"action_arguments": { | |
"newname": "snps_vcf_file" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "snpvcf" | |
} | |
}, | |
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0", | |
"tool_shed_repository": { | |
"changeset_revision": "5bbf9eada9c2", | |
"name": "snippy", | |
"owner": "iuc", | |
"tool_shed": "toolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"adv\": {\"mapqual\": \"60\", \"mincov\": \"10\", \"minfrac\": \"0.9\", \"minqual\": \"100.0\", \"rgid\": \"\", \"bwaopt\": \"\", \"rename_cons\": \"false\"}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"outvcf\", \"outgff\", \"outtab\", \"outsum\", \"outlog\", \"outaln\", \"outcon\"], \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "4.5.0", | |
"type": "tool", | |
"uuid": "954eafd8-5fcc-4eed-a53b-36cbc5c819fa", | |
"workflow_outputs": [] | |
}, | |
"4": { | |
"annotation": "", | |
"content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0", | |
"errors": null, | |
"id": 4, | |
"input_connections": { | |
"input1": { | |
"id": 3, | |
"output_name": "snpvcf" | |
} | |
}, | |
"inputs": [], | |
"label": "tb_variant_filter", | |
"name": "TB Variant Filter", | |
"outputs": [ | |
{ | |
"name": "output1", | |
"type": "vcf" | |
} | |
], | |
"position": { | |
"bottom": 596.1166839599609, | |
"height": 93.19999694824219, | |
"left": 389, | |
"right": 589, | |
"top": 502.91668701171875, | |
"width": 200, | |
"x": 389, | |
"y": 502.91668701171875 | |
}, | |
"post_job_actions": {}, | |
"tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0", | |
"tool_shed_repository": { | |
"changeset_revision": "fd1e41511caa", | |
"name": "tb_variant_filter", | |
"owner": "sanbi-uwc", | |
"tool_shed": "testtoolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"close_to_indel_filter\": \"true\", \"enable_region_filter\": \"true\", \"indel_window_size\": \"5\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"min_depth\": \"30\", \"min_depth_filter\": \"false\", \"min_percentage_alt\": \"90.0\", \"min_percentage_alt_filter\": \"true\", \"region_filter\": [\"pe_ppe\", \"uvp\"], \"snv_only_filter\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "0.1.3+galaxy0", | |
"type": "tool", | |
"uuid": "8ae2d4d1-ce93-44fa-9210-e0e1de2d0d4a", | |
"workflow_outputs": [ | |
{ | |
"label": null, | |
"output_name": "output1", | |
"uuid": "f1f1dba5-169f-4347-81c1-fd27d074d807" | |
} | |
] | |
}, | |
"5": { | |
"annotation": "", | |
"content_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/vcf_to_alignment/vcf_to_alignment/0.5", | |
"errors": null, | |
"id": 5, | |
"input_connections": { | |
"reference|history": { | |
"id": 0, | |
"output_name": "output" | |
}, | |
"vcf_inputs": { | |
"id": 4, | |
"output_name": "output1" | |
} | |
}, | |
"inputs": [], | |
"label": null, | |
"name": "Generate FASTA alignment from VCF collection", | |
"outputs": [ | |
{ | |
"name": "output_alignment", | |
"type": "fasta" | |
} | |
], | |
"position": { | |
"bottom": 685.7166748046875, | |
"height": 184.79998779296875, | |
"left": 844, | |
"right": 1044, | |
"top": 500.91668701171875, | |
"width": 200, | |
"x": 844, | |
"y": 500.91668701171875 | |
}, | |
"post_job_actions": { | |
"HideDatasetActionoutput_alignment": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "output_alignment" | |
}, | |
"RenameDatasetActionoutput_alignment": { | |
"action_arguments": { | |
"newname": "consensus_fasta.fasta" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "output_alignment" | |
} | |
}, | |
"tool_id": "testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/vcf_to_alignment/vcf_to_alignment/0.5", | |
"tool_shed_repository": { | |
"changeset_revision": "4f3f7d390382", | |
"name": "vcf_to_alignment", | |
"owner": "sanbi-uwc", | |
"tool_shed": "testtoolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"exclude_list\": {\"do_exclude\": \"no\", \"__current_case__\": 1}, \"reference\": {\"source\": \"history\", \"__current_case__\": 0, \"history\": {\"__class__\": \"ConnectedValue\"}}, \"remove_invariant_sites\": \"false\", \"vcf_inputs\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "0.5", | |
"type": "tool", | |
"uuid": "96df2cf9-525c-4489-974b-3b66113a01a3", | |
"workflow_outputs": [] | |
}, | |
"6": { | |
"annotation": "", | |
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0", | |
"errors": null, | |
"id": 6, | |
"input_connections": { | |
"input_fasta": { | |
"id": 5, | |
"output_name": "output_alignment" | |
} | |
}, | |
"inputs": [], | |
"label": null, | |
"name": "Finds SNP sites", | |
"outputs": [ | |
{ | |
"name": "output_fasta", | |
"type": "fasta" | |
} | |
], | |
"position": { | |
"bottom": 616.5166778564453, | |
"height": 113.59999084472656, | |
"left": 1533, | |
"right": 1733, | |
"top": 502.91668701171875, | |
"width": 200, | |
"x": 1533, | |
"y": 502.91668701171875 | |
}, | |
"post_job_actions": { | |
"HideDatasetActionoutput_fasta": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "output_fasta" | |
} | |
}, | |
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0", | |
"tool_shed_repository": { | |
"changeset_revision": "5804f786060d", | |
"name": "snp_sites", | |
"owner": "iuc", | |
"tool_shed": "toolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"input_fasta\": {\"__class__\": \"ConnectedValue\"}, \"out_type\": {\"ot_select\": \"alignment\", \"__current_case__\": 0, \"formats\": \"-m\", \"b\": \"false\", \"c\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "2.5.1+galaxy0", | |
"type": "tool", | |
"uuid": "e7445f46-0340-4295-b4bd-f1a18be056e0", | |
"workflow_outputs": [] | |
}, | |
"7": { | |
"annotation": "", | |
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0", | |
"errors": null, | |
"id": 7, | |
"input_connections": { | |
"input_fasta": { | |
"id": 5, | |
"output_name": "output_alignment" | |
} | |
}, | |
"inputs": [], | |
"label": null, | |
"name": "Finds SNP sites", | |
"outputs": [ | |
{ | |
"name": "output_counts", | |
"type": "tabular" | |
} | |
], | |
"position": { | |
"bottom": 778.9166870117188, | |
"height": 134, | |
"left": 1533, | |
"right": 1733, | |
"top": 644.9166870117188, | |
"width": 200, | |
"x": 1533, | |
"y": 644.9166870117188 | |
}, | |
"post_job_actions": { | |
"HideDatasetActionoutput_counts": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "output_counts" | |
} | |
}, | |
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0", | |
"tool_shed_repository": { | |
"changeset_revision": "5804f786060d", | |
"name": "snp_sites", | |
"owner": "iuc", | |
"tool_shed": "toolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"input_fasta\": {\"__class__\": \"ConnectedValue\"}, \"out_type\": {\"ot_select\": \"counts\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "2.5.1+galaxy0", | |
"type": "tool", | |
"uuid": "dcb341b9-7e65-4bf0-b1e2-c65a8784ec26", | |
"workflow_outputs": [] | |
}, | |
"8": { | |
"annotation": "", | |
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0", | |
"errors": null, | |
"id": 8, | |
"input_connections": { | |
"input": { | |
"id": 6, | |
"output_name": "output_fasta" | |
} | |
}, | |
"inputs": [], | |
"label": null, | |
"name": "SNP distance matrix", | |
"outputs": [ | |
{ | |
"name": "output", | |
"type": "tabular" | |
} | |
], | |
"position": { | |
"bottom": 455.3166809082031, | |
"height": 154.39999389648438, | |
"left": 2108, | |
"right": 2308, | |
"top": 300.91668701171875, | |
"width": 200, | |
"x": 2108, | |
"y": 300.91668701171875 | |
}, | |
"post_job_actions": {}, | |
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0", | |
"tool_shed_repository": { | |
"changeset_revision": "1959cc43b414", | |
"name": "snp_dists", | |
"owner": "iuc", | |
"tool_shed": "toolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"a\": \"false\", \"b\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"k\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "0.6.3+galaxy0", | |
"type": "tool", | |
"uuid": "aa64e540-c733-4d93-8b0a-7127a56435c8", | |
"workflow_outputs": [ | |
{ | |
"label": null, | |
"output_name": "output", | |
"uuid": "5c765980-75cd-4b46-b28d-2c0c6db4c242" | |
} | |
] | |
}, | |
"9": { | |
"annotation": "", | |
"content_id": "param_value_from_file", | |
"errors": null, | |
"id": 9, | |
"input_connections": { | |
"input1": { | |
"id": 7, | |
"output_name": "output_counts" | |
} | |
}, | |
"inputs": [], | |
"label": null, | |
"name": "Parse parameter value", | |
"outputs": [ | |
{ | |
"name": "text_param", | |
"type": "expression.json" | |
} | |
], | |
"position": { | |
"bottom": 850.3166809082031, | |
"height": 154.39999389648438, | |
"left": 1825, | |
"right": 2025, | |
"top": 695.9166870117188, | |
"width": 200, | |
"x": 1825, | |
"y": 695.9166870117188 | |
}, | |
"post_job_actions": { | |
"HideDatasetActiontext_param": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "text_param" | |
} | |
}, | |
"tool_id": "param_value_from_file", | |
"tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"text\", \"remove_newlines\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "0.1.0", | |
"type": "tool", | |
"uuid": "45c409dd-e0f3-4601-b582-6951c481ee46", | |
"workflow_outputs": [] | |
}, | |
"10": { | |
"annotation": "", | |
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1", | |
"errors": null, | |
"id": 10, | |
"input_connections": { | |
"general_options|s": { | |
"id": 6, | |
"output_name": "output_fasta" | |
}, | |
"miscellaneous_options|fconst": { | |
"id": 9, | |
"output_name": "text_param" | |
} | |
}, | |
"inputs": [ | |
{ | |
"description": "runtime parameter for tool IQ-TREE", | |
"name": "general_options" | |
}, | |
{ | |
"description": "runtime parameter for tool IQ-TREE", | |
"name": "general_options" | |
}, | |
{ | |
"description": "runtime parameter for tool IQ-TREE", | |
"name": "likelihood_mapping" | |
} | |
], | |
"label": null, | |
"name": "IQ-TREE", | |
"outputs": [ | |
{ | |
"name": "bionj", | |
"type": "nhx" | |
}, | |
{ | |
"name": "treefile", | |
"type": "nhx" | |
}, | |
{ | |
"name": "contree", | |
"type": "nhx" | |
}, | |
{ | |
"name": "mldist", | |
"type": "mldist" | |
}, | |
{ | |
"name": "splits.nex", | |
"type": "nex" | |
}, | |
{ | |
"name": "iqtree", | |
"type": "iqtree" | |
} | |
], | |
"position": { | |
"bottom": 1704.5166625976562, | |
"height": 1201.5999755859375, | |
"left": 2105, | |
"right": 2305, | |
"top": 502.91668701171875, | |
"width": 200, | |
"x": 2105, | |
"y": 502.91668701171875 | |
}, | |
"post_job_actions": { | |
"HideDatasetActionbionj": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "bionj" | |
}, | |
"HideDatasetActioncontree": { | |
"action_arguments": {}, | |
"action_type": "HideDatasetAction", | |
"output_name": "contree" | |
}, | |
"RenameDatasetActionbionj": { | |
"action_arguments": { | |
"newname": "iqtree_bionj_tree_file.nhx" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "bionj" | |
}, | |
"RenameDatasetActioncontree": { | |
"action_arguments": { | |
"newname": "iqtree_consconsensus_tree.nhx" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "contree" | |
}, | |
"RenameDatasetActioniqtree": { | |
"action_arguments": { | |
"newname": "iqtree_report_final_tree.iqtree" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "iqtree" | |
}, | |
"RenameDatasetActionmldist": { | |
"action_arguments": { | |
"newname": "iqtree_max_likeli_hood_distance_matrix.midist" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "mldist" | |
}, | |
"RenameDatasetActionsplits.nex": { | |
"action_arguments": { | |
"newname": "iqtree_frequencies_in_bootstrap_tree.nex" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "splits.nex" | |
}, | |
"RenameDatasetActiontreefile": { | |
"action_arguments": { | |
"newname": "iqtree_max_likeli_hood_tree.nhx" | |
}, | |
"action_type": "RenameDatasetAction", | |
"output_name": "treefile" | |
} | |
}, | |
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1", | |
"tool_shed_repository": { | |
"changeset_revision": "d1c340a5664b", | |
"name": "iqtree", | |
"owner": "iuc", | |
"tool_shed": "toolshed.g2.bx.psu.edu" | |
}, | |
"tool_state": "{\"bootstrap_parameters\": {\"ultrafast_bootstrap\": {\"bb\": \"1000\", \"wbt\": \"false\", \"wbtl\": \"false\", \"nm\": \"1000\", \"bcor\": \"0.99\", \"nstep\": \"100\", \"beps\": \"0.5\", \"bspec\": \"\", \"bnni\": \"false\"}, \"nonparametric_bootstrap\": {\"b\": \"\", \"bc\": \"false\", \"bo\": \"false\"}}, \"general_options\": {\"s\": {\"__class__\": \"ConnectedValue\"}, \"st\": \"DNA\", \"t\": {\"__class__\": \"RuntimeValue\"}, \"te\": {\"__class__\": \"RuntimeValue\"}, \"seed\": \"\", \"keep_ident\": \"false\", \"safe\": \"false\"}, \"likelihood_mapping\": {\"lmap\": \"\", \"lmclust\": {\"__class__\": \"RuntimeValue\"}, \"wql\": \"false\"}, \"miscellaneous_options\": {\"fconst\": {\"__class__\": \"ConnectedValue\"}}, \"modelling_parameters\": {\"automatic_model\": {\"cond_model\": {\"opt_custommodel\": \"false\", \"__current_case__\": 1, \"m\": \"\"}, \"rcluster\": \"\", \"mset\": \"\", \"msub\": \"nuclear\", \"mfreq\": \"\", \"mrate\": \"\", \"cmin\": \"2\", \"cmax\": \"10\", \"merit\": \"AIC\", \"mtree\": \"false\", \"madd\": \"\", \"mdef\": {\"__class__\": \"RuntimeValue\"}}, \"specifying_substitution\": {\"mwopt\": \"false\"}, \"rate_heterogeneity\": {\"a\": \"\", \"gmedian\": \"false\", \"i\": \"\", \"opt_gamma_inv\": \"false\", \"wsr\": \"false\"}, \"partition_model\": {\"q\": {\"__class__\": \"RuntimeValue\"}, \"spp\": \"false\", \"sp\": {\"__class__\": \"RuntimeValue\"}}, \"site_specific_frequency\": {\"ft\": {\"__class__\": \"RuntimeValue\"}, \"fs\": \"\", \"fmax\": \"false\"}}, \"tree_parameters\": {\"tree_search\": {\"n\": \"\", \"ninit\": \"100\", \"ntop\": \"20\", \"nbest\": \"5\", \"nstop\": \"100\", \"sprrad\": \"6\", \"pers\": \"0.5\", \"allnni\": \"false\", \"djc\": \"false\", \"g\": {\"__class__\": \"RuntimeValue\"}}, \"single_branch\": {\"alrt\": \"\", \"abayes\": \"false\", \"lbp\": \"\"}, \"tree_topology\": {\"z\": {\"__class__\": \"RuntimeValue\"}, \"zb\": \"\", \"zw\": \"false\", \"au\": \"false\"}, \"constructing_consensus\": {\"con\": \"false\", \"net\": \"false\", \"minsup\": \"0.0\", \"bi\": \"\", \"sup\": {\"__class__\": \"RuntimeValue\"}, \"suptag\": \"\"}, \"computing_robinson_foulds\": {\"rf\": {\"__class__\": \"RuntimeValue\"}, \"rf_all\": \"false\", \"rf_adj\": \"false\"}, \"generating_random\": {\"r\": \"\", \"ru\": \"false\", \"rcat\": \"false\", \"rbal\": \"false\", \"rcsg\": \"false\", \"rlen\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
"tool_version": "1.5.5.1", | |
"type": "tool", | |
"uuid": "db28e22f-5dd2-4fc2-bf6d-e857a1345818", | |
"workflow_outputs": [ | |
{ | |
"label": null, | |
"output_name": "iqtree", | |
"uuid": "bf7d7fc2-fa86-4271-83e5-8ae2642e6111" | |
}, | |
{ | |
"label": null, | |
"output_name": "mldist", | |
"uuid": "861cd649-4a7e-4964-b8b2-625cc9141766" | |
}, | |
{ | |
"label": null, | |
"output_name": "treefile", | |
"uuid": "90b9b486-26f9-4474-949a-aa78e9df2c2f" | |
}, | |
{ | |
"label": null, | |
"output_name": "splits.nex", | |
"uuid": "8aecaa9d-2c64-4045-a65c-bc42070a0569" | |
} | |
] | |
} | |
}, | |
"tags": [], | |
"uuid": "3c4aa699-282d-4577-887d-bb71682faef1", | |
"version": 7 | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment