Mercurial > repos > stemcellcommons > chipseq_workflows
changeset 5:4bf23bc4f4e2 draft
Update workflows and dependencies
| author | stemcellcommons |
|---|---|
| date | Fri, 22 Jul 2016 00:07:10 -0400 |
| parents | c9a9e3a09f44 |
| children | e6d80da34425 |
| files | 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 |
| diffstat | 4 files changed, 445 insertions(+), 108 deletions(-) [+] |
line wrap: on
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--- 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 @@ -27,7 +27,7 @@ "tool_state": "{\"name\": \"exp_file\"}", "tool_version": null, "type": "data_input", - "uuid": "dd984d64-daac-4547-9989-9303056523d3", + "uuid": "e1db5f1d-b05b-4ecd-a194-0a1b37eec5c3", "workflow_outputs": [] }, "1": { @@ -53,7 +53,7 @@ "tool_state": "{\"name\": \"input_file\"}", "tool_version": null, "type": "data_input", - "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", + "uuid": "369ab95a-3497-48c7-80c1-586ad71d8c14", "workflow_outputs": [] }, "2": { @@ -66,7 +66,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Parallel Groomer", + "name": "input_file" + } + ], "label": null, "name": "FASTQ Parallel Groomer", "outputs": [ @@ -82,10 +87,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", - "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\"}", + "tool_shed_repository": { + "changeset_revision": "66ca0d174cf2", + "name": "fastq_groomer_parallel", + "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_version": "0.3.1", "type": "tool", - "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", + "uuid": "b81ef5b7-b1dc-440d-a441-8ecd1953626d", "workflow_outputs": [] }, "3": { @@ -98,7 +109,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Parallel Groomer", + "name": "input_file" + } + ], "label": null, "name": "FASTQ Parallel Groomer", "outputs": [ @@ -114,10 +130,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", - "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\"}", + "tool_shed_repository": { + "changeset_revision": "66ca0d174cf2", + "name": "fastq_groomer_parallel", + "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_version": "0.3.1", "type": "tool", - "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", + "uuid": "9e279dc6-3a13-47e6-8252-148f3473a0fb", "workflow_outputs": [] }, "4": { @@ -130,7 +152,12 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with Bowtie for Illumina", + "name": "singlePaired" + } + ], "label": null, "name": "Map with Bowtie for Illumina", "outputs": [ @@ -162,10 +189,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__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_shed_repository": { + "changeset_revision": "df86f29bedee", + "name": "bowtie_wrappers", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__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_version": "1.1.3", "type": "tool", - 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"uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677", + "uuid": "9b5ea3b7-4c70-4dd1-91ac-0201897bfe74", "workflow_outputs": [] }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", "id": 6, "input_connections": { "source|input1": { @@ -226,7 +270,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool SAM-to-BAM", + "name": "source" + } + ], "label": null, "name": "SAM-to-BAM", "outputs": [ @@ -241,16 +290,22 @@ }, "post_job_actions": {}, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", - "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", + "tool_shed_repository": { + "changeset_revision": "d04d9f1c6791", + "name": "sam_to_bam", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "2.0", "type": "tool", - "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", + "uuid": "2e04c1f9-8079-4561-892d-c3e2c30e4702", "workflow_outputs": [] }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", "id": 7, "input_connections": { "source|input1": { @@ -258,7 +313,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool SAM-to-BAM", + "name": "source" + } + ], "label": null, "name": "SAM-to-BAM", "outputs": [ @@ -273,11 +333,17 @@ }, "post_job_actions": {}, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", - "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", + "tool_shed_repository": { + "changeset_revision": "d04d9f1c6791", + "name": "sam_to_bam", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "2.0", "type": "tool", - "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", + "uuid": "11a847f3-7d2e-44b2-9cd6-ee9285508002", "workflow_outputs": [] }, "8": { @@ -294,7 +360,16 @@ "output_name": "output1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MACS2 callpeak", + "name": "input_control_file" + }, + { + "description": "runtime parameter for tool MACS2 callpeak", + "name": "input_treatment_file" + } + ], "label": null, "name": "MACS2 callpeak", "outputs": [ @@ -342,10 +417,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", - "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__\\\": 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_shed_repository": { + "changeset_revision": "6d4babad010f", + "name": "macs2", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "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\": \"{\\\"__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_version": "2.1.0.20151222.0", "type": "tool", - "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", + "uuid": "ee77dbd1-6b19-4faa-bcb5-b71db4348aaa", "workflow_outputs": [] }, "9": { @@ -362,7 +443,16 @@ "output_name": "output_treat_pileup" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MACS2 bdgcmp", + "name": "infile_control" + }, + { + "description": "runtime parameter for tool MACS2 bdgcmp", + "name": "infile_treatment" + } + ], "label": null, "name": "MACS2 bdgcmp", "outputs": [ @@ -378,10 +468,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "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_shed_repository": { + "changeset_revision": "6d4babad010f", + "name": "macs2", + "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_version": "2.1.0.20151222.0", "type": "tool", - "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", + "uuid": "17a78c22-1f86-42bc-93e3-f0d05f8b8cb2", "workflow_outputs": [] }, "10": { @@ -394,7 +490,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", + "name": "input1" + } + ], "label": null, "name": "Wig/BedGraph-to-bigWig", "outputs": [ @@ -410,12 +511,12 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "wig_to_bigWig", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.1.0", "type": "tool", - "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", + "uuid": "909d96be-b7be-487e-b9e5-5e5b8e5126bd", "workflow_outputs": [] } }, - "uuid": "1008a9d1-09b6-465e-9515-6cad350b4089" + "uuid": "6a85dafd-cfde-4b35-988e-1bc4c0c93b94" } \ No newline at end of file
--- 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 @@ -6,6 +6,7 @@ "steps": { "0": { "annotation": "", + "content_id": null, "id": 0, "input_connections": {}, "inputs": [ @@ -14,6 +15,7 @@ "name": "exp_file" } ], + "label": null, "name": "Input dataset", "outputs": [], "position": { @@ -25,10 +27,12 @@ "tool_state": "{\"name\": \"exp_file\"}", "tool_version": null, "type": "data_input", - "user_outputs": [] + "uuid": "f48e77b8-7d87-4b9f-bac1-6bd9748addab", + "workflow_outputs": [] }, "1": { "annotation": "", + "content_id": null, "id": 1, "input_connections": {}, "inputs": [ @@ -37,6 +41,7 @@ "name": "input_file" } ], + "label": null, "name": "Input dataset", "outputs": [], "position": { @@ -48,10 +53,12 @@ "tool_state": "{\"name\": \"input_file\"}", "tool_version": null, "type": "data_input", - "user_outputs": [] + "uuid": "d38090b9-b25b-4fea-948e-f5818b1d2d4f", + "workflow_outputs": [] }, "2": { "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", "id": 2, "input_connections": { "input_file": { @@ -59,7 +66,13 @@ "output_name": "output" } }, - 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"user_outputs": [] + "uuid": "f5cf8c55-03d2-4fc0-b5fa-5f4be859b628", + "workflow_outputs": [] } - } + }, + "uuid": "9d3dbd7d-2fd7-479f-a582-aa2d84a5d443" } \ No newline at end of file
--- 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 @@ -27,7 +27,7 @@ "tool_state": "{\"name\": \"exp_file\"}", "tool_version": null, "type": "data_input", - "uuid": "dd984d64-daac-4547-9989-9303056523d3", + "uuid": "77699462-04dc-4480-a351-c3ba909c94d9", "workflow_outputs": [] }, "1": { @@ -53,7 +53,7 @@ "tool_state": "{\"name\": \"input_file\"}", "tool_version": null, "type": "data_input", - "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", + "uuid": "87084ec7-ede5-4f5a-a49c-5f96c169daa7", "workflow_outputs": [] }, "2": { @@ -66,7 +66,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Parallel Groomer", + "name": "input_file" + } + ], "label": null, "name": "FASTQ Parallel Groomer", "outputs": [ @@ -82,10 +87,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", - 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"inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool FASTQ Parallel Groomer", + "name": "input_file" + } + ], "label": null, "name": "FASTQ Parallel Groomer", "outputs": [ @@ -114,10 +130,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", - "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\"}", + "tool_shed_repository": { + "changeset_revision": "66ca0d174cf2", + "name": "fastq_groomer_parallel", + "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_version": "0.3.1", "type": "tool", - 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"uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", + "uuid": "5c875347-40cd-4522-a57a-ca380f976df4", "workflow_outputs": [] }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", "id": 7, "input_connections": { "source|input1": { @@ -258,7 +313,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool SAM-to-BAM", + "name": "source" + } + ], "label": null, "name": "SAM-to-BAM", "outputs": [ @@ -273,11 +333,17 @@ }, "post_job_actions": {}, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", - "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", + "tool_shed_repository": { + "changeset_revision": "d04d9f1c6791", + "name": "sam_to_bam", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "2.0", "type": "tool", - "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", + "uuid": "6f3e360c-d5b4-46bb-9a3d-e56c78651cee", "workflow_outputs": [] }, "8": { @@ -294,7 +360,16 @@ "output_name": "output1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MACS2 callpeak", + "name": "input_control_file" + }, + { + "description": "runtime parameter for tool MACS2 callpeak", + "name": "input_treatment_file" + } + ], "label": null, "name": "MACS2 callpeak", "outputs": [ @@ -342,10 +417,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", - "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\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "6d4babad010f", + "name": "macs2", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"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_version": "2.1.0.20151222.0", "type": "tool", - "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", + "uuid": "bbcb3034-f9af-4b45-b877-54822312ddac", "workflow_outputs": [] }, "9": { @@ -362,7 +443,16 @@ "output_name": "output_treat_pileup" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MACS2 bdgcmp", + "name": "infile_control" + }, + { + "description": "runtime parameter for tool MACS2 bdgcmp", + "name": "infile_treatment" + } + ], "label": null, "name": "MACS2 bdgcmp", "outputs": [ @@ -378,10 +468,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "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_shed_repository": { + "changeset_revision": "6d4babad010f", + "name": "macs2", + "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_version": "2.1.0.20151222.0", "type": "tool", - "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", + "uuid": "21c64164-b151-4bc4-88c8-3c3a68401a41", "workflow_outputs": [] }, "10": { @@ -394,7 +490,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", + "name": "input1" + } + ], "label": null, "name": "Wig/BedGraph-to-bigWig", "outputs": [ @@ -410,12 +511,12 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "wig_to_bigWig", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.1.0", "type": "tool", - "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", + "uuid": "de37a72c-ebc2-4f4f-9e80-70b11d1be79a", "workflow_outputs": [] } }, - "uuid": "a2493925-4c14-413d-89d6-0b3ba2395dbe" + "uuid": "3be7b1f8-3931-40c8-8bb1-7fffbe2826d4" } \ No newline at end of file
--- a/repository_dependencies.xml Tue Jul 19 14:44:20 2016 -0400 +++ b/repository_dependencies.xml Fri Jul 22 00:07:10 2016 -0400 @@ -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>