Repository 'str_fm'
hg clone https://toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm

Changeset 7:90021d286a67 (2015-08-24)
Previous changeset 6:d75894f5d61b (2015-08-22) Next changeset 8:808bd6c3ac71 (2015-08-24)
Commit message:
Deleted selected files
removed:
Galaxy-Workflow-microsatellite_profiling.ga
test-data/Galaxy-Workflow-microsatellite_profiling.ga
b
diff -r d75894f5d61b -r 90021d286a67 Galaxy-Workflow-microsatellite_profiling.ga
--- a/Galaxy-Workflow-microsatellite_profiling.ga Sat Aug 22 12:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,764 +0,0 @@\n-{\n-    "a_galaxy_workflow": "true", \n-    "annotation": "Profile length of microsatellites or short tandem repeats from short read data", \n-    "format-version": "0.1", \n-    "name": "microsatellite_profiling", \n-    "steps": {\n-        "0": {\n-            "annotation": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", \n-            "id": 0, \n-            "input_connections": {}, \n-            "inputs": [\n-                {\n-                    "description": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", \n-                    "name": "single end fastq"\n-                }\n-            ], \n-            "name": "Input dataset", \n-            "outputs": [], \n-            "position": {\n-                "left": 200, \n-                "top": 274.765625\n-            }, \n-            "tool_errors": null, \n-            "tool_id": null, \n-            "tool_state": "{\\"name\\": \\"single end fastq\\"}", \n-            "tool_version": null, \n-            "type": "data_input", \n-            "user_outputs": []\n-        }, \n-        "1": {\n-            "annotation": "need to be prepared by user using TR genome profiling", \n-            "id": 1, \n-            "input_connections": {}, \n-            "inputs": [\n-                {\n-                    "description": "need to be prepared by user using TR genome profiling", \n-                    "name": "TR in genome"\n-                }\n-            ], \n-            "name": "Input dataset", \n-            "outputs": [], \n-            "position": {\n-                "left": 177, \n-                "top": 412.953125\n-            }, \n-            "tool_errors": null, \n-            "tool_id": null, \n-            "tool_state": "{\\"name\\": \\"TR in genome\\"}", \n-            "tool_version": null, \n-            "type": "data_input", \n-            "user_outputs": []\n-        }, \n-        "2": {\n-            "annotation": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", \n-            "id": 2, \n-            "input_connections": {}, \n-            "inputs": [\n-                {\n-                    "description": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", \n-                    "name": "error rate file"\n-                }\n-            ], \n-            "name": "Input dataset", \n-            "outputs": [], \n-            "position": {\n-                "left": 1412.875, \n-                "top": 384.671875\n-            }, \n-            "tool_errors": null, \n-            "tool_id": null, \n-            "tool_state": "{\\"name\\": \\"error rate file\\"}", \n-            "tool_version": null, \n-            "type": "data_input", \n-            "user_outputs": []\n-        }, \n-        "3": {\n-            "annotation": "", \n-            "id": 3, \n-            "input_connections": {\n-                "filePath": {\n-                    "id": 0, \n-                    "output_name": "output"\n-                }\n-            }, \n-            "inputs": [], \n-            "name": "Microsatellite detection", \n-            "outputs": [\n-                {\n-                    "name": "stdout", \n-                    "type": "tabular"\n-                }\n-            ], \n-            "position": {\n-                "left": 441.953125, \n-                "top": 252\n-            }, \n-            "post_job_actions": {\n-                "ChangeDatatypeActionstdout": {\n-                    "action_arguments": {\n-                        "newtype": "tabular"\n-                    }, \n-                    "action_type": "ChangeDatatypeAction", \n-                    "output_name": "stdout"\n-                }, \n-                "RenameDatasetActionstdout": {\n-                    "action_arguments": {\n-                        "newname": "TR in raw reads"\n-                    }, \n-                    "action_type": "RenameDatasetAction", \n-                    "output_name": "stdout"\n-                }\n-            }, \n-            "tool_errors": null, \n-   '..b'          "HideDatasetActionout_file1": {\n-                    "action_arguments": {}, \n-                    "action_type": "HideDatasetAction", \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "tool_errors": null, \n-            "tool_id": "Grouping1", \n-            "tool_state": "{\\"operations\\": \\"[{\\\\\\"opcol\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"6\\\\\\"}, \\\\\\"__index__\\\\\\": 0, \\\\\\"optype\\\\\\": \\\\\\"cat\\\\\\", \\\\\\"opround\\\\\\": \\\\\\"no\\\\\\"}, {\\\\\\"opcol\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"4\\\\\\"}, \\\\\\"__index__\\\\\\": 1, \\\\\\"optype\\\\\\": \\\\\\"cat_uniq\\\\\\", \\\\\\"opround\\\\\\": \\\\\\"no\\\\\\"}]\\", \\"__page__\\": 0, \\"input1\\": \\"null\\", \\"ignorelines\\": \\"null\\", \\"groupcol\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"8\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"ignorecase\\": \\"\\\\\\"False\\\\\\"\\"}", \n-            "tool_version": "2.1.0", \n-            "type": "tool", \n-            "user_outputs": []\n-        }, \n-        "19": {\n-            "annotation": "", \n-            "id": 19, \n-            "input_connections": {\n-                "input": {\n-                    "id": 18, \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "inputs": [], \n-            "name": "Filter", \n-            "outputs": [\n-                {\n-                    "name": "out_file1", \n-                    "type": "input"\n-                }\n-            ], \n-            "position": {\n-                "left": 1186, \n-                "top": 1405.953125\n-            }, \n-            "post_job_actions": {\n-                "RenameDatasetActionout_file1": {\n-                    "action_arguments": {\n-                        "newname": "TR profile"\n-                    }, \n-                    "action_type": "RenameDatasetAction", \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "tool_errors": null, \n-            "tool_id": "Filter1", \n-            "tool_state": "{\\"input\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"header_lines\\": \\"\\\\\\"0\\\\\\"\\", \\"cond\\": \\"\\\\\\"c2.count(\\\\\\\\\\\\\\",\\\\\\\\\\\\\\")>=4\\\\\\"\\", \\"__page__\\": 0}", \n-            "tool_version": "1.1.0", \n-            "type": "tool", \n-            "user_outputs": []\n-        }, \n-        "20": {\n-            "annotation": "", \n-            "id": 20, \n-            "input_connections": {\n-                "microsat_error_profile": {\n-                    "id": 2, \n-                    "output_name": "output"\n-                }, \n-                "microsat_raw": {\n-                    "id": 19, \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "inputs": [], \n-            "name": "Correct genotype for microsatellite errors", \n-            "outputs": [\n-                {\n-                    "name": "microsat_corrected", \n-                    "type": "tabular"\n-                }\n-            ], \n-            "position": {\n-                "left": 1591.328125, \n-                "top": 456.8125\n-            }, \n-            "post_job_actions": {\n-                "RenameDatasetActionmicrosat_corrected": {\n-                    "action_arguments": {\n-                        "newname": "Genotype file"\n-                    }, \n-                    "action_type": "RenameDatasetAction", \n-                    "output_name": "microsat_corrected"\n-                }\n-            }, \n-            "tool_errors": null, \n-            "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/GenotypeSTR/2.0.0", \n-            "tool_state": "{\\"microsat_raw\\": \\"null\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"microsat_error_profile\\": \\"null\\", \\"expectedminorallele\\": \\"\\\\\\"0.5\\\\\\"\\"}", \n-            "tool_version": "2.0.0", \n-            "type": "tool", \n-            "user_outputs": []\n-        }\n-    }\n-}\n\\ No newline at end of file\n'
b
diff -r d75894f5d61b -r 90021d286a67 test-data/Galaxy-Workflow-microsatellite_profiling.ga
--- a/test-data/Galaxy-Workflow-microsatellite_profiling.ga Sat Aug 22 12:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,764 +0,0 @@\n-{\n-    "a_galaxy_workflow": "true", \n-    "annotation": "Profile length of microsatellites or short tandem repeats from short read data", \n-    "format-version": "0.1", \n-    "name": "microsatellite_profiling", \n-    "steps": {\n-        "0": {\n-            "annotation": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", \n-            "id": 0, \n-            "input_connections": {}, \n-            "inputs": [\n-                {\n-                    "description": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", \n-                    "name": "single end fastq"\n-                }\n-            ], \n-            "name": "Input dataset", \n-            "outputs": [], \n-            "position": {\n-                "left": 249, \n-                "top": 274.765625\n-            }, \n-            "tool_errors": null, \n-            "tool_id": null, \n-            "tool_state": "{\\"name\\": \\"single end fastq\\"}", \n-            "tool_version": null, \n-            "type": "data_input", \n-            "user_outputs": []\n-        }, \n-        "1": {\n-            "annotation": "need to be prepared by user using TR genome profiling", \n-            "id": 1, \n-            "input_connections": {}, \n-            "inputs": [\n-                {\n-                    "description": "need to be prepared by user using TR genome profiling", \n-                    "name": "STR in genome"\n-                }\n-            ], \n-            "name": "Input dataset", \n-            "outputs": [], \n-            "position": {\n-                "left": 226, \n-                "top": 412.953125\n-            }, \n-            "tool_errors": null, \n-            "tool_id": null, \n-            "tool_state": "{\\"name\\": \\"STR in genome\\"}", \n-            "tool_version": null, \n-            "type": "data_input", \n-            "user_outputs": []\n-        }, \n-        "2": {\n-            "annotation": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", \n-            "id": 2, \n-            "input_connections": {}, \n-            "inputs": [\n-                {\n-                    "description": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", \n-                    "name": "error rate file"\n-                }\n-            ], \n-            "name": "Input dataset", \n-            "outputs": [], \n-            "position": {\n-                "left": 1492.875, \n-                "top": 497.671875\n-            }, \n-            "tool_errors": null, \n-            "tool_id": null, \n-            "tool_state": "{\\"name\\": \\"error rate file\\"}", \n-            "tool_version": null, \n-            "type": "data_input", \n-            "user_outputs": []\n-        }, \n-        "3": {\n-            "annotation": "", \n-            "id": 3, \n-            "input_connections": {\n-                "filePath": {\n-                    "id": 0, \n-                    "output_name": "output"\n-                }\n-            }, \n-            "inputs": [], \n-            "name": "STR detection", \n-            "outputs": [\n-                {\n-                    "name": "stdout", \n-                    "type": "tabular"\n-                }\n-            ], \n-            "position": {\n-                "left": 515, \n-                "top": 256.5\n-            }, \n-            "post_job_actions": {\n-                "ChangeDatatypeActionstdout": {\n-                    "action_arguments": {\n-                        "newtype": "tabular"\n-                    }, \n-                    "action_type": "ChangeDatatypeAction", \n-                    "output_name": "stdout"\n-                }, \n-                "RenameDatasetActionstdout": {\n-                    "action_arguments": {\n-                        "newname": "STR in raw reads"\n-                    }, \n-                    "action_type": "RenameDatasetAction", \n-                    "output_name": "stdout"\n-                }\n-            }, \n-            "tool_errors": null, \n-            "too'..b' "post_job_actions": {\n-                "HideDatasetActionout_file1": {\n-                    "action_arguments": {}, \n-                    "action_type": "HideDatasetAction", \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "tool_errors": null, \n-            "tool_id": "Grouping1", \n-            "tool_state": "{\\"operations\\": \\"[{\\\\\\"opcol\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"6\\\\\\"}, \\\\\\"__index__\\\\\\": 0, \\\\\\"optype\\\\\\": \\\\\\"cat\\\\\\", \\\\\\"opround\\\\\\": \\\\\\"no\\\\\\"}, {\\\\\\"opcol\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"4\\\\\\"}, \\\\\\"__index__\\\\\\": 1, \\\\\\"optype\\\\\\": \\\\\\"cat_uniq\\\\\\", \\\\\\"opround\\\\\\": \\\\\\"no\\\\\\"}]\\", \\"__page__\\": 0, \\"input1\\": \\"null\\", \\"ignorelines\\": \\"null\\", \\"groupcol\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"8\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"ignorecase\\": \\"\\\\\\"False\\\\\\"\\"}", \n-            "tool_version": "2.1.0", \n-            "type": "tool", \n-            "user_outputs": []\n-        }, \n-        "19": {\n-            "annotation": "", \n-            "id": 19, \n-            "input_connections": {\n-                "input": {\n-                    "id": 18, \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "inputs": [], \n-            "name": "Filter", \n-            "outputs": [\n-                {\n-                    "name": "out_file1", \n-                    "type": "input"\n-                }\n-            ], \n-            "position": {\n-                "left": 1227, \n-                "top": 1406.953125\n-            }, \n-            "post_job_actions": {\n-                "RenameDatasetActionout_file1": {\n-                    "action_arguments": {\n-                        "newname": "STR profile"\n-                    }, \n-                    "action_type": "RenameDatasetAction", \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "tool_errors": null, \n-            "tool_id": "Filter1", \n-            "tool_state": "{\\"input\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"header_lines\\": \\"\\\\\\"0\\\\\\"\\", \\"cond\\": \\"\\\\\\"c2.count(\\\\\\\\\\\\\\",\\\\\\\\\\\\\\")>=4\\\\\\"\\", \\"__page__\\": 0}", \n-            "tool_version": "1.1.0", \n-            "type": "tool", \n-            "user_outputs": []\n-        }, \n-        "20": {\n-            "annotation": "", \n-            "id": 20, \n-            "input_connections": {\n-                "microsat_error_profile": {\n-                    "id": 2, \n-                    "output_name": "output"\n-                }, \n-                "microsat_raw": {\n-                    "id": 19, \n-                    "output_name": "out_file1"\n-                }\n-            }, \n-            "inputs": [], \n-            "name": "Correct genotype for STR errors", \n-            "outputs": [\n-                {\n-                    "name": "microsat_corrected", \n-                    "type": "tabular"\n-                }\n-            ], \n-            "position": {\n-                "left": 1673.5, \n-                "top": 561.5\n-            }, \n-            "post_job_actions": {\n-                "RenameDatasetActionmicrosat_corrected": {\n-                    "action_arguments": {\n-                        "newname": "Genotype file"\n-                    }, \n-                    "action_type": "RenameDatasetAction", \n-                    "output_name": "microsat_corrected"\n-                }\n-            }, \n-            "tool_errors": null, \n-            "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/GenotypeSTR/2.0.0", \n-            "tool_state": "{\\"microsat_raw\\": \\"null\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"microsat_error_profile\\": \\"null\\", \\"expectedminorallele\\": \\"\\\\\\"0.5\\\\\\"\\"}", \n-            "tool_version": "2.0.0", \n-            "type": "tool", \n-            "user_outputs": []\n-        }\n-    }\n-}\n\\ No newline at end of file\n'