Mercurial > repos > bgruening > glimmer_gene_calling_workflow
diff glimmer3_with_trainingset.ga @ 5:2405efd751a0 draft
Uploaded
author | bgruening |
---|---|
date | Mon, 12 Aug 2013 12:56:19 -0400 |
parents | 22bfc027a718 |
children | 9d5515db5920 |
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--- a/glimmer3_with_trainingset.ga Mon Aug 12 12:08:47 2013 -0400 +++ b/glimmer3_with_trainingset.ga Mon Aug 12 12:56:19 2013 -0400 @@ -17,8 +17,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 283, - "top": 376 + "left": 235.60880279541016, + "top": 214.3896484375 }, "tool_errors": null, "tool_id": null, @@ -40,8 +40,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 443, - "top": 232 + "left": 454.55167388916016, + "top": 215.35415649414062 }, "tool_errors": null, "tool_id": null, @@ -68,13 +68,19 @@ } ], "position": { - "left": 503, - "top": 486 + "left": 456.9629592895508, + "top": 555.8248291015625 }, - "post_job_actions": {}, + "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, \"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_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": [] @@ -109,19 +115,19 @@ } ], "position": { - "left": 674, - "top": 319 + "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\", \"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_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": "", + "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": { @@ -138,16 +144,16 @@ } ], "position": { - "left": 988, - "top": 351 + "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\": \"\\\"no\\\"\", \"table\": \"\\\"11\\\"\", \"alternative\": \"\\\"no\\\"\"}", + "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": [] } } -} +} \ No newline at end of file