Mercurial > repos > crs4 > glimmer
view Galaxy-Workflow-Glimmer.ga @ 0:9c8ffce71f7c draft default tip
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author | crs4 |
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date | Mon, 09 Sep 2013 12:16:17 -0400 |
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{ "a_galaxy_workflow": "true", "annotation": "glimmer-from-scratch", "format-version": "0.1", "name": "Glimmer", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Genome sequence" } ], "name": "Input dataset", "outputs": [], "position": { "left": 158, "top": 200 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Genome sequence\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "", "id": 1, "input_connections": { "loSequence": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "Long-ORFs", "outputs": [ { "name": "logfile", "type": "txt" }, { "name": "loOutput", "type": "glimmer_coords" } ], "position": { "left": 248, "top": 336 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "long-orfs_wrapper", "tool_state": "{\"loFixed\": \"\\\"False\\\"\", \"__page__\": 0, \"loMaxOverlap\": \"\\\"\\\"\", \"loMinLen\": \"\\\"\\\"\", \"loStartCodons\": \"\\\"\\\"\", \"loTransTable\": \"\\\"\\\"\", \"loNoHeader\": \"\\\"False\\\"\", \"loLengthOpt\": \"\\\"False\\\"\", \"loCutoff\": \"\\\"\\\"\", \"loStopCodons\": \"\\\"\\\"\", \"loLinear\": \"\\\"False\\\"\", \"loWithoutStops\": \"\\\"False\\\"\", \"loEntropy\": \"null\", \"loSequence\": \"null\"}", "tool_version": "0.2", "type": "tool", "user_outputs": [] }, "2": { "annotation": "", "id": 2, "input_connections": { "exCoords": { "id": 1, "output_name": "loOutput" }, "exSequence": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "Extract", "outputs": [ { "name": "logfile", "type": "txt" }, { "name": "exOutput", "type": "fasta" } ], "position": { "left": 659, "top": 231 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "extract_wrapper", "tool_state": "{\"__page__\": 0, \"exSequence\": \"null\", \"exCoords\": \"null\", \"exDir\": \"\\\"False\\\"\", \"exNoStop\": \"\\\"False\\\"\", \"exNoStart\": \"\\\"False\\\"\", \"exNoWrap\": \"\\\"False\\\"\", \"exMinLen\": \"\\\"\\\"\", \"ex2Fields\": \"\\\"False\\\"\"}", "tool_version": "0.2", "type": "tool", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": { "biSequence": { "id": 2, "output_name": "exOutput" } }, "inputs": [], "name": "Build-ICM", "outputs": [ { "name": "logfile", "type": "txt" }, { "name": "biIcm", "type": "glimmer_icm" } ], "position": { "left": 177, "top": 715 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "build-icm_wrapper", "tool_state": "{\"__page__\": 0, \"biStopCodons\": \"\\\"\\\"\", \"biPeriod\": \"\\\"3\\\"\", \"biTransTable\": \"\\\"\\\"\", \"biNoStops\": \"\\\"False\\\"\", \"biDepth\": \"\\\"7\\\"\", \"biReverse\": \"\\\"False\\\"\", \"biSequence\": \"null\", \"biWidth\": \"\\\"12\\\"\"}", "tool_version": "0.2", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "glIcm": { "id": 3, "output_name": "biIcm" }, "glSequence": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "Glimmer3", "outputs": [ { "name": "logfile", "type": "txt" }, { "name": "glDetail", "type": "txt" }, { "name": "glPredict", "type": "txt" } ], "position": { "left": 508, "top": 715 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "glimmer3_wrapper", "tool_state": "{\"__page__\": 0, \"glFirstCodon\": \"\\\"False\\\"\", \"glNoIndep\": \"\\\"False\\\"\", \"glIcm\": \"null\", \"glRbsPwm\": \"null\", \"glEntropy\": \"null\", \"glSeparateGenes\": \"\\\"False\\\"\", \"glOrfCoords\": \"null\", \"glMaxOverlap\": \"\\\"\\\"\", \"glIgnoreScoreLen\": \"\\\"\\\"\", \"glGcPercent\": \"\\\"\\\"\", \"glSequence\": \"null\", \"glGeneLen\": \"\\\"\\\"\", \"glStopCodons\": \"\\\"\\\"\", \"glExtend\": \"\\\"False\\\"\", \"glLinear\": \"\\\"False\\\"\", \"glTransTable\": \"\\\"\\\"\", \"glThreshold\": \"\\\"\\\"\", \"glStartCodons\": \"\\\"\\\"\", \"glStartProbs\": \"\\\"\\\"\"}", "tool_version": "0.2", "type": "tool", "user_outputs": [] } } }