# HG changeset patch # User stemcellcommons # Date 1469212409 14400 # Node ID e6d80da34425d99ae4c56cf19a80a8b39981aa36 # Parent 4bf23bc4f4e26cd754a738bdc63df48e07848a16 Uploaded a new version of hg19 diff -r 4bf23bc4f4e2 -r e6d80da34425 TF_ChIP-Seq_analysis_using_MACS2__hg19.ga --- a/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga Fri Jul 22 00:07:10 2016 -0400 +++ b/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga Fri Jul 22 14:33:29 2016 -0400 @@ -27,7 +27,7 @@ "tool_state": "{\"name\": \"exp_file\"}", "tool_version": null, "type": "data_input", - "uuid": "f48e77b8-7d87-4b9f-bac1-6bd9748addab", + "uuid": "dd984d64-daac-4547-9989-9303056523d3", "workflow_outputs": [] }, "1": { @@ -53,7 +53,7 @@ "tool_state": "{\"name\": \"input_file\"}", "tool_version": null, "type": "data_input", - "uuid": "d38090b9-b25b-4fea-948e-f5818b1d2d4f", + "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", "workflow_outputs": [] }, "2": { @@ -66,12 +66,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool FASTQ Parallel Groomer", - "name": "input_file" - } - ], + "inputs": [], "label": null, "name": "FASTQ Parallel Groomer", "outputs": [ @@ -93,10 +88,10 @@ "owner": "kevyin", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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\\\"}\"}", + "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\"}", "tool_version": "0.3.1", "type": "tool", - "uuid": "c2e08189-33e3-40bf-a914-cfdb726734e5", + "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", "workflow_outputs": [] }, "3": { @@ -109,12 +104,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool FASTQ Parallel Groomer", - "name": "input_file" - } - ], + "inputs": [], "label": null, "name": "FASTQ Parallel Groomer", "outputs": [ @@ -136,10 +126,10 @@ "owner": "kevyin", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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\\\"}\"}", + "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\"}", "tool_version": "0.3.1", "type": "tool", - "uuid": "7b72130c-3620-4406-b127-aa2d7a1323db", + "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", "workflow_outputs": [] }, "4": { @@ -152,12 +142,7 @@ "output_name": "output_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with Bowtie for Illumina", - "name": "singlePaired" - } - ], + "inputs": [], "label": null, "name": "Map with Bowtie for Illumina", "outputs": [ @@ -195,10 +180,10 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", + "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.1.3", "type": "tool", - "uuid": "c90992f7-766c-4395-b9c4-da4bd2e51840", + "uuid": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", "workflow_outputs": [] }, "5": { @@ -211,12 +196,7 @@ "output_name": "output_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with Bowtie for Illumina", - "name": "singlePaired" - } - ], + "inputs": [], "label": null, "name": "Map with Bowtie for Illumina", "outputs": [ @@ -254,10 +234,10 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", + "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.1.3", "type": "tool", - "uuid": "3d32d656-7912-44e6-a632-218286b7f916", + "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677", "workflow_outputs": [] }, "6": { @@ -270,12 +250,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool SAM-to-BAM", - "name": "source" - } - ], + "inputs": [], "label": null, "name": "SAM-to-BAM", "outputs": [ @@ -297,10 +272,10 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"hg19\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"hg19full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "2.0", "type": "tool", - "uuid": "7181b07a-7d15-4716-ae59-9a1084d445f3", + "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", "workflow_outputs": [] }, "7": { @@ -313,12 +288,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool SAM-to-BAM", - "name": "source" - } - ], + "inputs": [], "label": null, "name": "SAM-to-BAM", "outputs": [ @@ -340,14 +310,14 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"hg19\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"hg19full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "2.0", "type": "tool", - "uuid": "37977857-377d-4e5f-b256-fae093d920de", + "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", "workflow_outputs": [] }, "8": { - "annotation": "{\"output_tabular\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"tabular\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}", + "annotation": "{\"output_narrowpeaks\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"bed\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", "id": 8, "input_connections": { @@ -360,16 +330,7 @@ "output_name": "output1" } }, - "inputs": [ - { - "description": "runtime parameter for tool MACS2 callpeak", - "name": "input_control_file" - }, - { - "description": "runtime parameter for tool MACS2 callpeak", - "name": "input_treatment_file" - } - ], + "inputs": [], "label": null, "name": "MACS2 callpeak", "outputs": [ @@ -423,10 +384,10 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2451960000\\\", \\\"__current_case__\\\": 0}\", \"bampe\": \"\\\"false\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__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\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", + "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2451960000\\\", \\\"__current_case__\\\": 0}\", \"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\\\"\"}", "tool_version": "2.1.0.20151222.0", "type": "tool", - "uuid": "7d522e1b-10c7-41d6-8fee-455133c85089", + "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", "workflow_outputs": [] }, "9": { @@ -443,16 +404,7 @@ "output_name": "output_treat_pileup" } }, - "inputs": [ - { - "description": "runtime parameter for tool MACS2 bdgcmp", - "name": "infile_control" - }, - { - "description": "runtime parameter for tool MACS2 bdgcmp", - "name": "infile_treatment" - } - ], + "inputs": [], "label": null, "name": "MACS2 bdgcmp", "outputs": [ @@ -474,10 +426,10 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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\\\"}\"}", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", "tool_version": "2.1.0.20151222.0", "type": "tool", - "uuid": "dcfd9cac-e8a2-4425-a8fc-1e398710d6ca", + "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", "workflow_outputs": [] }, "10": { @@ -490,12 +442,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", - "name": "input1" - } - ], + "inputs": [], "label": null, "name": "Wig/BedGraph-to-bigWig", "outputs": [ @@ -511,12 +458,12 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "wig_to_bigWig", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.1.0", "type": "tool", - "uuid": "f5cf8c55-03d2-4fc0-b5fa-5f4be859b628", + "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", "workflow_outputs": [] } }, - "uuid": "9d3dbd7d-2fd7-479f-a582-aa2d84a5d443" + "uuid": "f9305594-34b1-4189-b59f-9f217a9d9b34" } \ No newline at end of file