Mercurial > repos > arkarachai-fungtammasan > fakename
diff Galaxy-Workflow-Estimate_minimum_informative_read_depth.ga @ 0:70f8259b0b30 draft
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author | arkarachai-fungtammasan |
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date | Wed, 01 Apr 2015 16:48:58 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-Estimate_minimum_informative_read_depth.ga Wed Apr 01 16:48:58 2015 -0400 @@ -0,0 +1,342 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Estimate minimum informative read depth", + "steps": { + "0": { + "annotation": "See sample in https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "See sample in https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", + "name": "TR error rate" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 220, + "top": 737 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"TR error rate\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "replace 'A' with motif of interest", + "id": 1, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 385, + "top": 260 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4=='A'\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "error_profile": { + "id": 1, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Generate all possible combination of read profile", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 653.5, + "top": 203 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/Profilegenerator/2.0.0", + "tool_state": "{\"error_profile\": \"null\", \"MOTIF\": \"\\\"A\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"minprob\": \"\\\"1e-08\\\"\", \"Maxdepth\": \"\\\"30\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "Unique", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 676, + "top": 322 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3", + "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"False\\\"\", \"input\": \"null\"}", + "tool_version": "0.3", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "microsat_error_profile": { + "id": 0, + "output_name": "output" + }, + "microsat_raw": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [], + "name": "Correct genotype for microsatellite errors", + "outputs": [ + { + "name": "microsat_corrected", + "type": "tabular" + } + ], + "position": { + "left": 661, + "top": 427 + }, + "post_job_actions": { + "HideDatasetActionmicrosat_corrected": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "microsat_corrected" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/GenotypeSTR/2.0.0", + "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "microsat_corrected" + } + }, + "inputs": [], + "name": "Select", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 732, + "top": 629 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Grep1", + "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"pattern\": \"\\\"hetero\\\"\"}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "replace 1 with motif size. 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