Mercurial > repos > arkarachai-fungtammasan > microsatellite_ngs

changeset 1:f265e26ab550

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Uploaded
author arkarachai-fungtammasan
date Fri, 24 Oct 2014 15:44:34 -0400
parents 20ab85af9505
children c12db4ec1619
files test-data/Galaxy-Workflow-Estimate_minimum_informative_read_depth.ga
diffstat 1 files changed, 342 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Galaxy-Workflow-Estimate_minimum_informative_read_depth.ga	Fri Oct 24 15:44:34 2014 -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. For example, if motif is AAG, use 3", 
+            "id": 6, 
+            "input_connections": {
+                "input": {
+                    "id": 5, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 746, 
+                "top": 783
+            }, 
+            "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\": \"\\\"abs(c7-c8)==1\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "microsat_error_profile": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "microsat_raw": {
+                    "id": 6, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Evaluate the probability of the allele combination to generate read profile", 
+            "outputs": [
+                {
+                    "name": "microsat_corrected", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 708.5, 
+                "top": 913
+            }, 
+            "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/heteroprob/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": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input": {
+                    "id": 7, 
+                    "output_name": "microsat_corrected"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sort", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 761, 
+                "top": 1133
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "sort1", 
+            "tool_state": "{\"__page__\": 0, \"style\": \"\\\"num\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"12\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", 
+            "tool_version": "1.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "input": {
+                    "id": 8, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Combine probability to generate read profile ", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 722, 
+                "top": 1264
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/combineproballelecom/2.0.0", 
+            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
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