| Previous changeset 6:e6d80da34425 (2016-07-22) Next changeset 8:358360fdeea9 (2017-10-24) |
|
Commit message:
Update all workflows |
|
modified:
TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga TF_ChIP-Seq_analysis_using_MACS2__mm10.ga |
| b |
| diff -r e6d80da34425 -r f9ffbe563402 TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga --- a/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga Fri Jul 22 14:33:29 2016 -0400 +++ b/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga Fri Jul 22 14:41:07 2016 -0400 |
| [ |
| b'@@ -27,7 +27,7 @@\n "tool_state": "{\\"name\\": \\"exp_file\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "e1db5f1d-b05b-4ecd-a194-0a1b37eec5c3", \n+ "uuid": "dd984d64-daac-4547-9989-9303056523d3", \n "workflow_outputs": []\n }, \n "1": {\n@@ -53,7 +53,7 @@\n "tool_state": "{\\"name\\": \\"input_file\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "369ab95a-3497-48c7-80c1-586ad71d8c14", \n+ "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", \n "workflow_outputs": []\n }, \n "2": {\n@@ -66,12 +66,7 @@\n "output_name": "output"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool FASTQ Parallel Groomer", \n- "name": "input_file"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "FASTQ Parallel Groomer", \n "outputs": [\n@@ -93,10 +88,10 @@\n "owner": "kevyin", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n- "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"null\\"}", \n "tool_version": "0.3.1", \n "type": "tool", \n- "uuid": "b81ef5b7-b1dc-440d-a441-8ecd1953626d", \n+ "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", \n "workflow_outputs": []\n }, \n "3": {\n@@ -109,12 +104,7 @@\n "output_name": "output"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool FASTQ Parallel Groomer", \n- "name": "input_file"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "FASTQ Parallel Groomer", \n "outputs": [\n@@ -136,10 +126,10 @@\n "owner": "kevyin", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n- "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"null\\"}", \n "tool_version": "0.3.1", \n "type": "tool", \n- "uuid": "9e279dc6-3a13-47e6-8252-148f3473a0fb", \n+ "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", \n "workflow_outputs": []\n }, \n "4": {\n@@ -152,12 +142,7 @@\n "ou'..b'e__\\": 0, \\"effective_genome_size_options\\": \\"{\\\\\\"gsize\\\\\\": \\\\\\"1400000000\\\\\\", \\\\\\"effective_genome_size_options_selector\\\\\\": \\\\\\"user_defined\\\\\\", \\\\\\"__current_case__\\\\\\": 4}\\", \\"bampe\\": \\"\\\\\\"false\\\\\\"\\", \\"input_control_file\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"outputs\\": \\"[\\\\\\"peaks_tabular\\\\\\", \\\\\\"bdg\\\\\\", \\\\\\"pdf\\\\\\"]\\", \\"cutoff_options\\": \\"{\\\\\\"cutoff_options_selector\\\\\\": \\\\\\"qvalue\\\\\\", \\\\\\"qvalue\\\\\\": \\\\\\"0.05\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"advanced_options\\": \\"{\\\\\\"advanced_options_selector\\\\\\": \\\\\\"off\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"input_treatment_file\\": \\"null\\", \\"nomodel_type\\": \\"{\\\\\\"nomodel_type_selector\\\\\\": \\\\\\"create_model\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"band_width\\": \\"\\\\\\"300\\\\\\"\\"}", \n "tool_version": "2.1.0.20151222.0", \n "type": "tool", \n- "uuid": "ee77dbd1-6b19-4faa-bcb5-b71db4348aaa", \n+ "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", \n "workflow_outputs": []\n }, \n "9": {\n@@ -443,16 +404,7 @@\n "output_name": "output_treat_pileup"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool MACS2 bdgcmp", \n- "name": "infile_control"\n- }, \n- {\n- "description": "runtime parameter for tool MACS2 bdgcmp", \n- "name": "infile_treatment"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "MACS2 bdgcmp", \n "outputs": [\n@@ -474,10 +426,10 @@\n "owner": "iuc", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n- "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"infile_control\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"bdgcmp_options\\": \\"{\\\\\\"bdgcmp_options_selector\\\\\\": \\\\\\"ppois\\\\\\", \\\\\\"__current_case__\\\\\\": 3}\\", \\"infile_treatment\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"infile_control\\": \\"null\\", \\"bdgcmp_options\\": \\"{\\\\\\"bdgcmp_options_selector\\\\\\": \\\\\\"ppois\\\\\\", \\\\\\"__current_case__\\\\\\": 3}\\", \\"infile_treatment\\": \\"null\\"}", \n "tool_version": "2.1.0.20151222.0", \n "type": "tool", \n- "uuid": "17a78c22-1f86-42bc-93e3-f0d05f8b8cb2", \n+ "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", \n "workflow_outputs": []\n }, \n "10": {\n@@ -490,12 +442,7 @@\n "output_name": "outfile"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", \n- "name": "input1"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "Wig/BedGraph-to-bigWig", \n "outputs": [\n@@ -511,12 +458,12 @@\n "post_job_actions": {}, \n "tool_errors": null, \n "tool_id": "wig_to_bigWig", \n- "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"settings\\": \\"{\\\\\\"settingsType\\\\\\": \\\\\\"preset\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\", \\"settings\\": \\"{\\\\\\"settingsType\\\\\\": \\\\\\"preset\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n "tool_version": "1.1.0", \n "type": "tool", \n- "uuid": "909d96be-b7be-487e-b9e5-5e5b8e5126bd", \n+ "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", \n "workflow_outputs": []\n }\n }, \n- "uuid": "6a85dafd-cfde-4b35-988e-1bc4c0c93b94"\n+ "uuid": "0838c78b-f387-440c-a3ac-c26e1f096f08"\n }\n\\ No newline at end of file\n' |
| b |
| diff -r e6d80da34425 -r f9ffbe563402 TF_ChIP-Seq_analysis_using_MACS2__mm10.ga --- a/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga Fri Jul 22 14:33:29 2016 -0400 +++ b/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga Fri Jul 22 14:41:07 2016 -0400 |
| [ |
| b'@@ -27,7 +27,7 @@\n "tool_state": "{\\"name\\": \\"exp_file\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "77699462-04dc-4480-a351-c3ba909c94d9", \n+ "uuid": "dd984d64-daac-4547-9989-9303056523d3", \n "workflow_outputs": []\n }, \n "1": {\n@@ -53,7 +53,7 @@\n "tool_state": "{\\"name\\": \\"input_file\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "87084ec7-ede5-4f5a-a49c-5f96c169daa7", \n+ "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", \n "workflow_outputs": []\n }, \n "2": {\n@@ -66,12 +66,7 @@\n "output_name": "output"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool FASTQ Parallel Groomer", \n- "name": "input_file"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "FASTQ Parallel Groomer", \n "outputs": [\n@@ -93,10 +88,10 @@\n "owner": "kevyin", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n- "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"null\\"}", \n "tool_version": "0.3.1", \n "type": "tool", \n- "uuid": "a91fcfa1-2ad2-4d1b-af4e-8c348ca99cf4", \n+ "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", \n "workflow_outputs": []\n }, \n "3": {\n@@ -109,12 +104,7 @@\n "output_name": "output"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool FASTQ Parallel Groomer", \n- "name": "input_file"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "FASTQ Parallel Groomer", \n "outputs": [\n@@ -136,10 +126,10 @@\n "owner": "kevyin", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n- "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"null\\"}", \n "tool_version": "0.3.1", \n "type": "tool", \n- "uuid": "93829f40-3abf-4aa3-8951-46b67cf86a95", \n+ "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", \n "workflow_outputs": []\n }, \n "4": {\n@@ -152,12 +142,7 @@\n "ou'..b'\n+ "tool_state": "{\\"__page__\\": 0, \\"effective_genome_size_options\\": \\"{\\\\\\"effective_genome_size_options_selector\\\\\\": \\\\\\"2150570000\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"bampe\\": \\"\\\\\\"false\\\\\\"\\", \\"input_control_file\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"outputs\\": \\"[\\\\\\"peaks_tabular\\\\\\", \\\\\\"bdg\\\\\\", \\\\\\"pdf\\\\\\"]\\", \\"cutoff_options\\": \\"{\\\\\\"cutoff_options_selector\\\\\\": \\\\\\"qvalue\\\\\\", \\\\\\"qvalue\\\\\\": \\\\\\"0.05\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"advanced_options\\": \\"{\\\\\\"advanced_options_selector\\\\\\": \\\\\\"off\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"input_treatment_file\\": \\"null\\", \\"nomodel_type\\": \\"{\\\\\\"nomodel_type_selector\\\\\\": \\\\\\"create_model\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"band_width\\": \\"\\\\\\"300\\\\\\"\\"}", \n "tool_version": "2.1.0.20151222.0", \n "type": "tool", \n- "uuid": "bbcb3034-f9af-4b45-b877-54822312ddac", \n+ "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", \n "workflow_outputs": []\n }, \n "9": {\n@@ -443,16 +404,7 @@\n "output_name": "output_treat_pileup"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool MACS2 bdgcmp", \n- "name": "infile_control"\n- }, \n- {\n- "description": "runtime parameter for tool MACS2 bdgcmp", \n- "name": "infile_treatment"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "MACS2 bdgcmp", \n "outputs": [\n@@ -474,10 +426,10 @@\n "owner": "iuc", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n- "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"infile_control\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"bdgcmp_options\\": \\"{\\\\\\"bdgcmp_options_selector\\\\\\": \\\\\\"ppois\\\\\\", \\\\\\"__current_case__\\\\\\": 3}\\", \\"infile_treatment\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"infile_control\\": \\"null\\", \\"bdgcmp_options\\": \\"{\\\\\\"bdgcmp_options_selector\\\\\\": \\\\\\"ppois\\\\\\", \\\\\\"__current_case__\\\\\\": 3}\\", \\"infile_treatment\\": \\"null\\"}", \n "tool_version": "2.1.0.20151222.0", \n "type": "tool", \n- "uuid": "21c64164-b151-4bc4-88c8-3c3a68401a41", \n+ "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", \n "workflow_outputs": []\n }, \n "10": {\n@@ -490,12 +442,7 @@\n "output_name": "outfile"\n }\n }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", \n- "name": "input1"\n- }\n- ], \n+ "inputs": [], \n "label": null, \n "name": "Wig/BedGraph-to-bigWig", \n "outputs": [\n@@ -511,12 +458,12 @@\n "post_job_actions": {}, \n "tool_errors": null, \n "tool_id": "wig_to_bigWig", \n- "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"settings\\": \\"{\\\\\\"settingsType\\\\\\": \\\\\\"preset\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\", \\"settings\\": \\"{\\\\\\"settingsType\\\\\\": \\\\\\"preset\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n "tool_version": "1.1.0", \n "type": "tool", \n- "uuid": "de37a72c-ebc2-4f4f-9e80-70b11d1be79a", \n+ "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", \n "workflow_outputs": []\n }\n }, \n- "uuid": "3be7b1f8-3931-40c8-8bb1-7fffbe2826d4"\n+ "uuid": "39cc71c7-4bc2-4aae-8d0b-579055f1e196"\n }\n\\ No newline at end of file\n' |