Mercurial > repos > bgruening > glimmer_gene_calling_workflow
view glimmer3_with_trainingset.ga @ 6:9d5515db5920 draft default tip
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author | bgruening |
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date | Fri, 23 Aug 2013 02:54:15 -0400 |
parents | 2405efd751a0 |
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{ "a_galaxy_workflow": "true", "annotation": "Runs Glimmer3 to predict genes in microbial DNA using a training set of known genes.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gene_calling_workflow\" target=\"_blank\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock et al. 2013).", "format-version": "0.1", "name": "Glimmer gene calling with trainingset.", "steps": { "0": { "annotation": "Nucleotide FASTA file of gene sequences used to train the gene calling of glimmer.", "id": 0, "input_connections": {}, "inputs": [ { "description": "Nucleotide FASTA file of gene sequences used to train the gene calling of glimmer.", "name": "Set of Genes" } ], "name": "Input dataset", "outputs": [], "position": { "left": 235.60880279541016, "top": 214.3896484375 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Set of Genes\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "Nucleotide FASTA file of genomic DNA (e.g. assembled contigs) to find genes in.", "id": 1, "input_connections": {}, "inputs": [ { "description": "Nucleotide FASTA file of genomic DNA (e.g. assembled contigs) to find genes in.", "name": "Input Genomic Sequence" } ], "name": "Input dataset", "outputs": [], "position": { "left": 454.55167388916016, "top": 215.35415649414062 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Genomic Sequence\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "2": { "annotation": "", "id": 2, "input_connections": { "infile": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "Glimmer ICM builder", "outputs": [ { "name": "outfile", "type": "data" } ], "position": { "left": 456.9629592895508, "top": 555.8248291015625 }, "post_job_actions": { "HideDatasetActionoutfile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outfile" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"7\\\"\", \"period\": \"\\\"3\\\"\", \"width\": \"\\\"12\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"no_stops\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}", "tool_version": "0.2", "type": "tool", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": { "icm_input": { "id": 2, "output_name": "outfile" }, "seq_input": { "id": 1, "output_name": "output" } }, "inputs": [], "name": "Glimmer3", "outputs": [ { "name": "genes_output", "type": "fasta" }, { "name": "report_output", "type": "txt" }, { "name": "detailed_output", "type": "txt" } ], "position": { "left": 696.1604690551758, "top": 341.2222137451172 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2", "tool_state": "{\"extend\": \"\\\"False\\\"\", \"__page__\": 0, \"linear\": \"\\\"True\\\"\", \"detailed_report\": \"\\\"False\\\"\", \"seq_input\": \"null\", \"__rerun_remap_job_id__\": null, \"gc_percent\": \"\\\"0.0\\\"\", \"start_codons\": \"\\\"atg,gtg,ttg\\\"\", \"threshold\": \"\\\"30\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"max_olap\": \"\\\"50\\\"\", \"no_indep\": \"\\\"False\\\"\", \"gene_len\": \"\\\"90\\\"\", \"report\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"icm_input\": \"null\"}", "tool_version": "0.2", "type": "tool", "user_outputs": [] }, "4": { "annotation": "We expect our input sequences to have a trailing stop codon, but do not want the star character in the protein output.", "id": 4, "input_connections": { "input1": { "id": 3, "output_name": "genes_output" } }, "inputs": [], "name": "transeq", "outputs": [ { "name": "out_file1", "type": "fasta" } ], "position": { "left": 981.725227355957, "top": 212.04936981201172 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": 0, \"input1\": \"null\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"yes\\\"\", \"table\": \"\\\"11\\\"\", \"alternative\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "5.0.0", "type": "tool", "user_outputs": [] } } }