Mercurial > repos > arkarachai-fungtammasan > str_fm
view Galaxy-Workflow-microsatellite_profiling.ga @ 10:d423f0de87b7 draft
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author | arkarachai-fungtammasan |
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date | Fri, 04 Sep 2015 09:57:51 -0400 |
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{ "a_galaxy_workflow": "true", "annotation": "Profile length of microsatellites or short tandem repeats from short read data", "format-version": "0.1", "name": "microsatellite_profiling", "steps": { "0": { "annotation": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", "id": 0, "input_connections": {}, "inputs": [ { "description": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", "name": "single end fastq" } ], "name": "Input dataset", "outputs": [], "position": { "left": 249, "top": 274.765625 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"single end fastq\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "need to be prepared by user using TR genome profiling", "id": 1, "input_connections": {}, "inputs": [ { "description": "need to be prepared by user using TR genome profiling", "name": "STR in genome" } ], "name": "Input dataset", "outputs": [], "position": { "left": 226, "top": 412.953125 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"STR in genome\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "2": { "annotation": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", "id": 2, "input_connections": {}, "inputs": [ { "description": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", "name": "error rate file" } ], "name": "Input dataset", "outputs": [], "position": { "left": 1492.875, "top": 497.671875 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"error rate file\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": { "filePath": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "STR detection", "outputs": [ { "name": "stdout", "type": "tabular" } ], "position": { "left": 515, "top": 256.5 }, "post_job_actions": { "ChangeDatatypeActionstdout": { "action_arguments": { "newtype": "tabular" }, "action_type": "ChangeDatatypeAction", "output_name": "stdout" }, "RenameDatasetActionstdout": { "action_arguments": { "newname": "STR in raw reads" }, "action_type": "RenameDatasetAction", "output_name": "stdout" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0", "tool_state": "{\"__page__\": 0, \"flankSetting\": \"{\\\"noflankdisplay\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"filePath\": \"null\", \"minlength\": \"\\\"5\\\"\", \"hammingThreshold\": \"\\\"0\\\"\", \"period\": \"\\\"1\\\"\", \"surfix\": \"\\\"20\\\"\", \"prefix\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"inputFileSource\": \"{\\\"inputFileType\\\": \\\"fastq\\\", \\\"__current_case__\\\": 3}\", \"partialmotifs\": \"\\\"True\\\"\", \"multipleruns\": \"\\\"True\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "input": { "id": 3, "output_name": "stdout" } }, "inputs": [], "name": "Read name modifier", "outputs": [ { "name": "output", "type": "tabular" } ], "position": { "left": 478, "top": 370 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/space2underscore_readname/1.0.0", "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"6\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "5": { "annotation": "", "id": 5, "input_connections": { "microsat_in_read": { "id": 4, "output_name": "output" } }, "inputs": [], "name": "Fetch bases flanking", "outputs": [ { "name": "Leftflanking", "type": "fastq" }, { "name": "Rightflanking", "type": "fastq" } ], "position": { "left": 446.5, "top": 503.5 }, "post_job_actions": { "ChangeDatatypeActionLeftflanking": { "action_arguments": { "newtype": "fastqsanger" }, "action_type": "ChangeDatatypeAction", "output_name": "Leftflanking" }, "ChangeDatatypeActionRightflanking": { "action_arguments": { "newtype": "fastqsanger" }, "action_type": "ChangeDatatypeAction", "output_name": "Rightflanking" }, "HideDatasetActionLeftflanking": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "Leftflanking" }, "HideDatasetActionRightflanking": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "Rightflanking" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/fetchflank/1.0.0", "tool_state": "{\"qualitycutoff\": \"\\\"20\\\"\", \"lengthofbasetocheckquality\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"microsat_in_read\": \"null\", \"__page__\": 0}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "6": { "annotation": "this tool has problems with parameter setting when you run it from pipeline. 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