| Previous changeset 4:c9a9e3a09f44 (2016-07-19) Next changeset 6:e6d80da34425 (2016-07-22) |
|
Commit message:
Update workflows and dependencies |
|
modified:
TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga TF_ChIP-Seq_analysis_using_MACS2__hg19.ga TF_ChIP-Seq_analysis_using_MACS2__mm10.ga repository_dependencies.xml |
| b |
| diff -r c9a9e3a09f44 -r 4bf23bc4f4e2 TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga --- a/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga Tue Jul 19 14:44:20 2016 -0400 +++ b/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga Fri Jul 22 00:07:10 2016 -0400 |
| [ |
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| b |
| diff -r c9a9e3a09f44 -r 4bf23bc4f4e2 TF_ChIP-Seq_analysis_using_MACS2__hg19.ga --- a/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga Tue Jul 19 14:44:20 2016 -0400 +++ b/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga Fri Jul 22 00:07:10 2016 -0400 |
| [ |
| b'@@ -6,6 +6,7 @@\n "steps": {\n "0": {\n "annotation": "", \n+ "content_id": null, \n "id": 0, \n "input_connections": {}, \n "inputs": [\n@@ -14,6 +15,7 @@\n "name": "exp_file"\n }\n ], \n+ "label": null, \n "name": "Input dataset", \n "outputs": [], \n "position": {\n@@ -25,10 +27,12 @@\n "tool_state": "{\\"name\\": \\"exp_file\\"}", \n "tool_version": null, \n "type": "data_input", \n- "user_outputs": []\n+ "uuid": "f48e77b8-7d87-4b9f-bac1-6bd9748addab", \n+ "workflow_outputs": []\n }, \n "1": {\n "annotation": "", \n+ "content_id": null, \n "id": 1, \n "input_connections": {}, \n "inputs": [\n@@ -37,6 +41,7 @@\n "name": "input_file"\n }\n ], \n+ "label": null, \n "name": "Input dataset", \n "outputs": [], \n "position": {\n@@ -48,10 +53,12 @@\n "tool_state": "{\\"name\\": \\"input_file\\"}", \n "tool_version": null, \n "type": "data_input", \n- "user_outputs": []\n+ "uuid": "d38090b9-b25b-4fea-948e-f5818b1d2d4f", \n+ "workflow_outputs": []\n }, \n "2": {\n "annotation": "", \n+ 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| b |
| diff -r c9a9e3a09f44 -r 4bf23bc4f4e2 TF_ChIP-Seq_analysis_using_MACS2__mm10.ga --- a/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga Tue Jul 19 14:44:20 2016 -0400 +++ b/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga Fri Jul 22 00:07:10 2016 -0400 |
| [ |
| b'@@ -27,7 +27,7 @@\n "tool_state": "{\\"name\\": \\"exp_file\\"}", \n "tool_version": null, \n "type": "data_input", \n- "uuid": "dd984d64-daac-4547-9989-9303056523d3", \n+ "uuid": "77699462-04dc-4480-a351-c3ba909c94d9", \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": "7a325193-5665-4aaf-9b87-c719769f9b71", \n+ "uuid": "87084ec7-ede5-4f5a-a49c-5f96c169daa7", \n "workflow_outputs": []\n }, \n "2": {\n@@ -66,7 +66,12 @@\n "output_name": "output"\n }\n }, \n- "inputs": [], \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool FASTQ Parallel Groomer", \n+ "name": "input_file"\n+ }\n+ ], \n "label": null, \n "name": "FASTQ Parallel Groomer", \n "outputs": [\n@@ -82,10 +87,16 @@\n "post_job_actions": {}, \n "tool_errors": null, \n "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n- "tool_state": 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\\\\\\"__current_case__\\\\\\": 3}\\", \\"infile_treatment\\": \\"null\\"}", \n+ "tool_shed_repository": {\n+ "changeset_revision": "6d4babad010f", \n+ "name": "macs2", \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_version": "2.1.0.20151222.0", \n "type": "tool", \n- "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", \n+ "uuid": "21c64164-b151-4bc4-88c8-3c3a68401a41", \n "workflow_outputs": []\n }, \n "10": {\n@@ -394,7 +490,12 @@\n "output_name": "outfile"\n }\n }, \n- "inputs": [], \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", \n+ "name": "input1"\n+ }\n+ ], \n "label": null, \n "name": "Wig/BedGraph-to-bigWig", \n "outputs": [\n@@ -410,12 +511,12 @@\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\\": \\"null\\", \\"settings\\": \\"{\\\\\\"settingsType\\\\\\": \\\\\\"preset\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"settings\\": \\"{\\\\\\"settingsType\\\\\\": \\\\\\"preset\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n "tool_version": "1.1.0", \n "type": "tool", \n- "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", \n+ "uuid": "de37a72c-ebc2-4f4f-9e80-70b11d1be79a", \n "workflow_outputs": []\n }\n }, \n- "uuid": "a2493925-4c14-413d-89d6-0b3ba2395dbe"\n+ "uuid": "3be7b1f8-3931-40c8-8bb1-7fffbe2826d4"\n }\n\\ No newline at end of file\n' |
| b |
| diff -r c9a9e3a09f44 -r 4bf23bc4f4e2 repository_dependencies.xml --- a/repository_dependencies.xml Tue Jul 19 14:44:20 2016 -0400 +++ b/repository_dependencies.xml Fri Jul 22 00:07:10 2016 -0400 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<repositories description="Stem Cell Commons TF ChIP-seq workflow for hg19"> +<repositories description="Stem Cell Commons TF ChIP-seq workflows"> <repository toolshed="toolshed.g2.bx.psu.edu" name="fastq_groomer_parallel" owner="kevyin" changeset_revision="66ca0d174cf2" /> <repository toolshed="toolshed.g2.bx.psu.edu" name="bowtie_wrappers" owner="devteam" changeset_revision="df86f29bedee" /> - <repository toolshed="toolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="881e16ad05c6" /> + <repository toolshed="toolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="d04d9f1c6791" /> <repository toolshed="toolshed.g2.bx.psu.edu" name="macs2" owner="iuc" changeset_revision="6d4babad010f" /> </repositories> |