Repository 'chipseq_workflows'
hg clone https://toolshed.g2.bx.psu.edu/repos/stemcellcommons/chipseq_workflows

Changeset 3:cfae7747e902 (2016-05-02)
Previous changeset 2:d60e070af736 (2016-04-28) Next changeset 4:c9a9e3a09f44 (2016-07-19)
Commit message:
Add workflows for mm10 and danRer7
added:
TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga
TF_ChIP-Seq_analysis_using_MACS2__mm10.ga
b
diff -r d60e070af736 -r cfae7747e902 TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga Mon May 02 21:07:29 2016 -0400
[
b'@@ -0,0 +1,421 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "{\\"refinery_type\\": \\"analysis\\", \\"refinery_relationships\\": [{\\"category\\": \\"1-1\\", \\"set1\\": \\"input_file\\", \\"set2\\": \\"exp_file\\"}]}", \n+    "format-version": "0.1", \n+    "name": "TF ChIP-Seq analysis using MACS2: mm10", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "exp_file"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 206, \n+                "top": 381.265625\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"exp_file\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "dd984d64-daac-4547-9989-9303056523d3", \n+            "workflow_outputs": []\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "input_file"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 201, \n+                "top": 516.265625\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"input_file\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", \n+            "workflow_outputs": []\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 2, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "fastqsanger"\n+                }\n+            ], \n+            "position": {\n+                "left": 422, \n+                "top": 341.265625\n+            }, \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": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"null\\"}", \n+            "tool_version": "0.3.1", \n+            "type": "tool", \n+            "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", \n+            "workflow_outputs": []\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 3, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 1, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+        '..b'      "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", \n+            "tool_state": "{\\"__page__\\": 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__\\\\\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b
diff -r d60e070af736 -r cfae7747e902 TF_ChIP-Seq_analysis_using_MACS2__mm10.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga Mon May 02 21:07:29 2016 -0400
[
b'@@ -0,0 +1,421 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "{\\"refinery_type\\": \\"analysis\\", \\"refinery_relationships\\": [{\\"category\\": \\"1-1\\", \\"set1\\": \\"input_file\\", \\"set2\\": \\"exp_file\\"}]}", \n+    "format-version": "0.1", \n+    "name": "TF ChIP-Seq analysis using MACS2: mm10", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "exp_file"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 206, \n+                "top": 381.265625\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"exp_file\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "dd984d64-daac-4547-9989-9303056523d3", \n+            "workflow_outputs": []\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "input_file"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 201, \n+                "top": 516.265625\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"input_file\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", \n+            "workflow_outputs": []\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 2, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "fastqsanger"\n+                }\n+            ], \n+            "position": {\n+                "left": 422, \n+                "top": 341.265625\n+            }, \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": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"output_type\\\\\\": \\\\\\"sanger\\\\\\", \\\\\\"force_quality_encoding\\\\\\": \\\\\\"ascii\\\\\\", \\\\\\"options_type_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"summarize_input\\\\\\": \\\\\\"dont_summarize_input\\\\\\"}\\", \\"input_file\\": \\"null\\"}", \n+            "tool_version": "0.3.1", \n+            "type": "tool", \n+            "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", \n+            "workflow_outputs": []\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 3, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 1, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+        '..b'"top": 358.5\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", \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": "e8e38d74-1a63-4c58-b042-487838e9edc7", \n+            "workflow_outputs": []\n+        }, \n+        "9": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", \n+            "id": 9, \n+            "input_connections": {\n+                "infile_control": {\n+                    "id": 8, \n+                    "output_name": "output_control_lambda"\n+                }, \n+                "infile_treatment": {\n+                    "id": 8, \n+                    "output_name": "output_treat_pileup"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "MACS2 bdgcmp", \n+            "outputs": [\n+                {\n+                    "name": "outfile", \n+                    "type": "bedgraph"\n+                }\n+            ], \n+            "position": {\n+                "left": 1648, \n+                "top": 426.5\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", \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": "974626f2-7adb-4f71-9db5-7abdff78e5d0", \n+            "workflow_outputs": []\n+        }, \n+        "10": {\n+            "annotation": "{\\"out_file1\\": {\\"name\\": \\"MACS2_bigwig\\", \\"description\\": \\"\\", \\"type\\": \\"bigwig\\"}}", \n+            "content_id": "wig_to_bigWig", \n+            "id": 10, \n+            "input_connections": {\n+                "input1": {\n+                    "id": 9, \n+                    "output_name": "outfile"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Wig/BedGraph-to-bigWig", \n+            "outputs": [\n+                {\n+                    "name": "out_file1", \n+                    "type": "bigwig"\n+                }\n+            ], \n+            "position": {\n+                "left": 1853.046875, \n+                "top": 447.71875\n+            }, \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_version": "1.1.0", \n+            "type": "tool", \n+            "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", \n+            "workflow_outputs": []\n+        }\n+    }, \n+    "uuid": "a2493925-4c14-413d-89d6-0b3ba2395dbe"\n+}\n\\ No newline at end of file\n'