Mercurial > repos > stemcellcommons > chipseq_workflows
changeset 8:358360fdeea9 draft
Update annotation
| author | stemcellcommons |
|---|---|
| date | Tue, 24 Oct 2017 16:48:56 -0400 |
| parents | f9ffbe563402 |
| children | 4b0ceb4c5971 |
| files | ChIP-seq_Peak_Calling_-_Human.ga ChIP-seq_Peak_Calling_-_Mouse.ga ChIP-seq_Peak_Calling_-_Zebrafish.ga 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 | 7 files changed, 1792 insertions(+), 1407 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ChIP-seq_Peak_Calling_-_Human.ga Tue Oct 24 16:48:56 2017 -0400 @@ -0,0 +1,597 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\n\t\"description\": \"Identify enriched regions (peaks) in ChIP-seq data. Reads are aligned to the human (hg19) reference genome.\",\n\t\"file_relationship\": {\n\t\t\"value_type\": \"LIST\",\n\t\t\"name\": \"List of FASTQ Pairs\",\n\t\t\"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Paired FASTQ files\",\n\t\t\t\"input_files\": [{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Treatment FASTQ\",\n\t\t\t\t\t\"description\": \"Treatment FASTQ\"\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Control FASTQ\",\n\t\t\t\t\t\"description\": \"Control FASTQ\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}", + "format-version": "0.1", + "name": "ChIP-seq Peak Calling - Human", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 179, + "top": 378.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"paired\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "5b809271-cb75-49d8-af55-a0bca0e01a87", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "b8721384-d8eb-42a1-a902-86c214339fbf" + } + ] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "id": 1, + "input_connections": { + "input_collection": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Split Paired Collection", + "outputs": [ + { + "name": "forward_element", + "type": "data" + }, + { + "name": "reverse_element", + "type": "data" + } + ], + "position": { + "left": 453.5, + "top": 400.5 + }, + "post_job_actions": { + "ChangeDatatypeActionforward_element": { + "action_arguments": { + "newtype": "fastqsanger" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "forward_element" + }, + "ChangeDatatypeActionreverse_element": { + "action_arguments": { + "newtype": "fastqsanger" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "reverse_element" + }, + "HideDatasetActionforward_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "forward_element" + }, + "HideDatasetActionreverse_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "reverse_element" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_collection\": \"null\"}", + "tool_version": "0.2", + "type": "tool", + "uuid": "af4cc45c-3f36-4bfd-8a2b-53af785bf24f", + "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": { + "id": 1, + "output_name": "forward_element" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 762.5, + "top": 341.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, + "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_version": "0.3.1", + "type": "tool", + "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 3, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "reverse_element" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 763.5, + "top": 493.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, + "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_version": "0.3.1", + "type": "tool", + "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", + "id": 4, + "input_connections": { + "singlePaired|sInput1": { + "id": 2, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Map with Bowtie for Illumina", + "outputs": [ + { + "name": "output", + "type": "sam" + }, + { + "name": "output_suppressed_reads_l", + "type": "fastq" + }, + { + "name": "output_suppressed_reads_r", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_l", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_r", + "type": "fastq" + } + ], + "position": { + "left": 1096, + "top": 272.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "HideDatasetActionoutput_suppressed_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_l" + }, + "HideDatasetActionoutput_suppressed_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_r" + }, + "HideDatasetActionoutput_unmapped_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_l" + }, + "HideDatasetActionoutput_unmapped_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_r" + } + }, + "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\\\": \\\"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": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", + "id": 5, + "input_connections": { + "singlePaired|sInput1": { + "id": 3, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Map with Bowtie for Illumina", + "outputs": [ + { + "name": "output", + "type": "sam" + }, + { + "name": "output_suppressed_reads_l", + "type": "fastq" + }, + { + "name": "output_suppressed_reads_r", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_l", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_r", + "type": "fastq" + } + ], + "position": { + "left": 1100, + "top": 492.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "HideDatasetActionoutput_suppressed_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_l" + }, + "HideDatasetActionoutput_suppressed_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_r" + }, + "HideDatasetActionoutput_unmapped_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_l" + }, + "HideDatasetActionoutput_unmapped_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_r" + } + }, + "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\\\": \\\"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": "a09286be-e5ba-45fb-be1f-585fe79cf677", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "id": 6, + "input_connections": { + "source|input1": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1410, + "top": 376.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "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\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19full\\\"}, \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "2.1", + "type": "tool", + "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "id": 7, + "input_connections": { + "source|input1": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1412, + "top": 533.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "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\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19full\\\"}, \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "2.1", + "type": "tool", + "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\"}}", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", + "id": 8, + "input_connections": { + "input_control_file": { + "id": 7, + "output_name": "output1" + }, + "input_treatment_file": { + "id": 6, + "output_name": "output1" + } + }, + "inputs": [], + "label": null, + "name": "MACS2 callpeak", + "outputs": [ + { + "name": "output_tabular", + "type": "tabular" + }, + { + "name": "output_broadpeaks", + "type": "bed" + }, + { + "name": "output_gappedpeaks", + "type": "bed" + }, + { + "name": "output_narrowpeaks", + "type": "bed" + }, + { + "name": "output_summits", + "type": "bed" + }, + { + "name": "output_plot", + "type": "pdf" + }, + { + "name": "output_treat_pileup", + "type": "bedgraph" + }, + { + "name": "output_control_lambda", + "type": "bedgraph" + }, + { + "name": "output_extra_files", + "type": "html" + } + ], + "position": { + "left": 1651, + "top": 358.5 + }, + "post_job_actions": { + "HideDatasetActionoutput_broadpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_broadpeaks" + }, + "HideDatasetActionoutput_control_lambda": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_control_lambda" + }, + "HideDatasetActionoutput_extra_files": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_extra_files" + }, + "HideDatasetActionoutput_gappedpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_gappedpeaks" + }, + "HideDatasetActionoutput_narrowpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_narrowpeaks" + }, + "HideDatasetActionoutput_summits": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_summits" + }, + "HideDatasetActionoutput_tabular": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_tabular" + }, + "HideDatasetActionoutput_treat_pileup": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_treat_pileup" + } + }, + "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\\\": \\\"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": "e8e38d74-1a63-4c58-b042-487838e9edc7", + "workflow_outputs": [ + { + "label": null, + "output_name": "output_plot", + "uuid": "736e98ec-fda0-42f0-84d4-938a0209afb9" + } + ] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", + "id": 9, + "input_connections": { + "infile_control": { + "id": 8, + "output_name": "output_control_lambda" + }, + "infile_treatment": { + "id": 8, + "output_name": "output_treat_pileup" + } + }, + "inputs": [], + "label": null, + "name": "MACS2 bdgcmp", + "outputs": [ + { + "name": "outfile", + "type": "bedgraph" + } + ], + "position": { + "left": 1988.5, + "top": 426.5 + }, + "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_version": "2.1.0.20151222.0", + "type": "tool", + "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", + "workflow_outputs": [ + { + "label": null, + "output_name": "outfile", + "uuid": "9a8230d5-c946-408b-ab03-4ae650e7b63a" + } + ] + }, + "10": { + "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", + "content_id": "wig_to_bigWig", + "id": 10, + "input_connections": { + "input1": { + "id": 9, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Wig/BedGraph-to-bigWig", + "outputs": [ + { + "name": "out_file1", + "type": "bigwig" + } + ], + "position": { + "left": 2193.546875, + "top": 447.71875 + }, + "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_version": "1.1.0", + "type": "tool", + "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", + "workflow_outputs": [ + { + "label": null, + "output_name": "out_file1", + "uuid": "a80f65d8-00af-423b-8d4f-f18ab017af23" + } + ] + } + }, + "uuid": "8f6742c5-3339-440e-93eb-70b4d7d3b99f" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ChIP-seq_Peak_Calling_-_Mouse.ga Tue Oct 24 16:48:56 2017 -0400 @@ -0,0 +1,597 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\n\t\"description\": \"Identify enriched regions (peaks) in ChIP-seq data. Reads are aligned to the mouse (mm10) reference genome.\",\n\t\"file_relationship\": {\n\t\t\"value_type\": \"LIST\",\n\t\t\"name\": \"List of FASTQ Pairs\",\n\t\t\"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Paired FASTQ files\",\n\t\t\t\"input_files\": [{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Treatment FASTQ\",\n\t\t\t\t\t\"description\": \"Treatment FASTQ\"\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Control FASTQ\",\n\t\t\t\t\t\"description\": \"Control FASTQ\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}", + "format-version": "0.1", + "name": "ChIP-seq Peak Calling - Mouse", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 200, + "top": 395.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"paired\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "356ec3d6-e4d4-442c-bbd6-84acab454f1a", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f6218906-b7d9-45d0-8d2a-1eb96c3e9a8e" + } + ] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "id": 1, + "input_connections": { + "input_collection": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Split Paired Collection", + "outputs": [ + { + "name": "forward_element", + "type": "data" + }, + { + "name": "reverse_element", + "type": "data" + } + ], + "position": { + "left": 474.5, + "top": 376.5 + }, + "post_job_actions": { + "ChangeDatatypeActionforward_element": { + "action_arguments": { + "newtype": "fastqsanger" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "forward_element" + }, + "ChangeDatatypeActionreverse_element": { + "action_arguments": { + "newtype": "fastqsanger" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "reverse_element" + }, + "HideDatasetActionforward_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "forward_element" + }, + "HideDatasetActionreverse_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "reverse_element" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_collection\": \"null\"}", + "tool_version": "0.2", + "type": "tool", + "uuid": "0b53727d-3d55-470e-b8d4-3d4a38fbfdf5", + "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": { + "id": 1, + "output_name": "forward_element" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 775.5, + "top": 342.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, + "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_version": "0.3.1", + "type": "tool", + "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 3, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "reverse_element" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 776.5, + "top": 494.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, + "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_version": "0.3.1", + "type": "tool", + "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", + "id": 4, + "input_connections": { + "singlePaired|sInput1": { + "id": 2, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Map with Bowtie for Illumina", + "outputs": [ + { + "name": "output", + "type": "sam" + }, + { + "name": "output_suppressed_reads_l", + "type": "fastq" + }, + { + "name": "output_suppressed_reads_r", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_l", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_r", + "type": "fastq" + } + ], + "position": { + "left": 1109, + "top": 273.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "HideDatasetActionoutput_suppressed_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_l" + }, + "HideDatasetActionoutput_suppressed_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_r" + }, + "HideDatasetActionoutput_unmapped_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_l" + }, + "HideDatasetActionoutput_unmapped_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_r" + } + }, + "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\\\": \\\"mm10\\\", \\\"__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": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", + "id": 5, + "input_connections": { + "singlePaired|sInput1": { + "id": 3, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Map with Bowtie for Illumina", + "outputs": [ + { + "name": "output", + "type": "sam" + }, + { + "name": "output_suppressed_reads_l", + "type": "fastq" + }, + { + "name": "output_suppressed_reads_r", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_l", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_r", + "type": "fastq" + } + ], + "position": { + "left": 1113, + "top": 493.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "HideDatasetActionoutput_suppressed_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_l" + }, + "HideDatasetActionoutput_suppressed_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_r" + }, + "HideDatasetActionoutput_unmapped_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_l" + }, + "HideDatasetActionoutput_unmapped_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_r" + } + }, + "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\\\": \\\"mm10\\\", \\\"__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": "a09286be-e5ba-45fb-be1f-585fe79cf677", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "id": 6, + "input_connections": { + "source|input1": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1424, + "top": 377.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "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", + "type": "tool", + "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "id": 7, + "input_connections": { + "source|input1": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1425, + "top": 534.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "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", + "type": "tool", + "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\"}}", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", + "id": 8, + "input_connections": { + "input_control_file": { + "id": 7, + "output_name": "output1" + }, + "input_treatment_file": { + "id": 6, + "output_name": "output1" + } + }, + "inputs": [], + "label": null, + "name": "MACS2 callpeak", + "outputs": [ + { + "name": "output_tabular", + "type": "tabular" + }, + { + "name": "output_broadpeaks", + "type": "bed" + }, + { + "name": "output_gappedpeaks", + "type": "bed" + }, + { + "name": "output_narrowpeaks", + "type": "bed" + }, + { + "name": "output_summits", + "type": "bed" + }, + { + "name": "output_plot", + "type": "pdf" + }, + { + "name": "output_treat_pileup", + "type": "bedgraph" + }, + { + "name": "output_control_lambda", + "type": "bedgraph" + }, + { + "name": "output_extra_files", + "type": "html" + } + ], + "position": { + "left": 1664, + "top": 359.5 + }, + "post_job_actions": { + "HideDatasetActionoutput_broadpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_broadpeaks" + }, + "HideDatasetActionoutput_control_lambda": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_control_lambda" + }, + "HideDatasetActionoutput_extra_files": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_extra_files" + }, + "HideDatasetActionoutput_gappedpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_gappedpeaks" + }, + "HideDatasetActionoutput_narrowpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_narrowpeaks" + }, + "HideDatasetActionoutput_summits": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_summits" + }, + "HideDatasetActionoutput_tabular": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_tabular" + }, + "HideDatasetActionoutput_treat_pileup": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_treat_pileup" + } + }, + "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_version": "2.1.0.20151222.0", + "type": "tool", + "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", + "workflow_outputs": [ + { + "label": null, + "output_name": "output_plot", + "uuid": "456fea9e-c16f-4baa-af2f-e22a65cc6b7f" + } + ] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", + "id": 9, + "input_connections": { + "infile_control": { + "id": 8, + "output_name": "output_control_lambda" + }, + "infile_treatment": { + "id": 8, + "output_name": "output_treat_pileup" + } + }, + "inputs": [], + "label": null, + "name": "MACS2 bdgcmp", + "outputs": [ + { + "name": "outfile", + "type": "bedgraph" + } + ], + "position": { + "left": 2001.5, + "top": 427.5 + }, + "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_version": "2.1.0.20151222.0", + "type": "tool", + "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", + "workflow_outputs": [ + { + "label": null, + "output_name": "outfile", + "uuid": "9b313409-0812-495c-848b-aaab5eaf05b4" + } + ] + }, + "10": { + "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", + "content_id": "wig_to_bigWig", + "id": 10, + "input_connections": { + "input1": { + "id": 9, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Wig/BedGraph-to-bigWig", + "outputs": [ + { + "name": "out_file1", + "type": "bigwig" + } + ], + "position": { + "left": 2243.546875, + "top": 432.71875 + }, + "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_version": "1.1.0", + "type": "tool", + "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", + "workflow_outputs": [ + { + "label": null, + "output_name": "out_file1", + "uuid": "5bbfca2d-617f-43d8-8eb9-a4d6a9a07eb8" + } + ] + } + }, + "uuid": "99c95324-e964-41d7-90fe-7c70d06942cf" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ChIP-seq_Peak_Calling_-_Zebrafish.ga Tue Oct 24 16:48:56 2017 -0400 @@ -0,0 +1,597 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\n\t\"description\": \"Identify enriched regions (peaks) in ChIP-seq data. Reads are aligned to the zebrafish (danRer7) reference genome.\",\n\t\"file_relationship\": {\n\t\t\"value_type\": \"LIST\",\n\t\t\"name\": \"List of FASTQ Pairs\",\n\t\t\"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Paired FASTQ files\",\n\t\t\t\"input_files\": [{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Treatment FASTQ\",\n\t\t\t\t\t\"description\": \"Treatment FASTQ\"\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Control FASTQ\",\n\t\t\t\t\t\"description\": \"Control FASTQ\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}", + "format-version": "0.1", + "name": "ChIP-seq Peak Calling - Zebrafish", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 227, + "top": 404.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"paired\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "69e8d98a-a949-4cc1-bbb7-99c434e6bdd0", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5116f669-b430-4381-922a-89142af20c13" + } + ] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "id": 1, + "input_connections": { + "input_collection": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Split Paired Collection", + "outputs": [ + { + "name": "forward_element", + "type": "data" + }, + { + "name": "reverse_element", + "type": "data" + } + ], + "position": { + "left": 551.5, + "top": 386.5 + }, + "post_job_actions": { + "ChangeDatatypeActionforward_element": { + "action_arguments": { + "newtype": "fastqsanger" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "forward_element" + }, + "ChangeDatatypeActionreverse_element": { + "action_arguments": { + "newtype": "fastqsanger" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "reverse_element" + }, + "HideDatasetActionforward_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "forward_element" + }, + "HideDatasetActionreverse_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "reverse_element" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_collection\": \"null\"}", + "tool_version": "0.2", + "type": "tool", + "uuid": "6c3e4f5d-d6f5-439f-8d16-c7b6ca5075de", + "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": { + "id": 1, + "output_name": "forward_element" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 861.5, + "top": 341.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, + "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_version": "0.3.1", + "type": "tool", + "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 3, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "reverse_element" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 862.5, + "top": 493.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, + "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_version": "0.3.1", + "type": "tool", + "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", + "id": 4, + "input_connections": { + "singlePaired|sInput1": { + "id": 2, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Map with Bowtie for Illumina", + "outputs": [ + { + "name": "output", + "type": "sam" + }, + { + "name": "output_suppressed_reads_l", + "type": "fastq" + }, + { + "name": "output_suppressed_reads_r", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_l", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_r", + "type": "fastq" + } + ], + "position": { + "left": 1195, + "top": 272.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "HideDatasetActionoutput_suppressed_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_l" + }, + "HideDatasetActionoutput_suppressed_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_r" + }, + "HideDatasetActionoutput_unmapped_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_l" + }, + "HideDatasetActionoutput_unmapped_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_r" + } + }, + "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_version": "1.1.3", + "type": "tool", + "uuid": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", + "id": 5, + "input_connections": { + "singlePaired|sInput1": { + "id": 3, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Map with Bowtie for Illumina", + "outputs": [ + { + "name": "output", + "type": "sam" + }, + { + "name": "output_suppressed_reads_l", + "type": "fastq" + }, + { + "name": "output_suppressed_reads_r", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_l", + "type": "fastq" + }, + { + "name": "output_unmapped_reads_r", + "type": "fastq" + } + ], + "position": { + "left": 1199, + "top": 492.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "HideDatasetActionoutput_suppressed_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_l" + }, + "HideDatasetActionoutput_suppressed_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_suppressed_reads_r" + }, + "HideDatasetActionoutput_unmapped_reads_l": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_l" + }, + "HideDatasetActionoutput_unmapped_reads_r": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_unmapped_reads_r" + } + }, + "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_version": "1.1.3", + "type": "tool", + "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "id": 6, + "input_connections": { + "source|input1": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1510, + "top": 376.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "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", + "type": "tool", + "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", + "id": 7, + "input_connections": { + "source|input1": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1511, + "top": 533.265625 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "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", + "type": "tool", + "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\"}}", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", + "id": 8, + "input_connections": { + "input_control_file": { + "id": 7, + "output_name": "output1" + }, + "input_treatment_file": { + "id": 6, + "output_name": "output1" + } + }, + "inputs": [], + "label": null, + "name": "MACS2 callpeak", + "outputs": [ + { + "name": "output_tabular", + "type": "tabular" + }, + { + "name": "output_broadpeaks", + "type": "bed" + }, + { + "name": "output_gappedpeaks", + "type": "bed" + }, + { + "name": "output_narrowpeaks", + "type": "bed" + }, + { + "name": "output_summits", + "type": "bed" + }, + { + "name": "output_plot", + "type": "pdf" + }, + { + "name": "output_treat_pileup", + "type": "bedgraph" + }, + { + "name": "output_control_lambda", + "type": "bedgraph" + }, + { + "name": "output_extra_files", + "type": "html" + } + ], + "position": { + "left": 1750, + "top": 358.5 + }, + "post_job_actions": { + "HideDatasetActionoutput_broadpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_broadpeaks" + }, + "HideDatasetActionoutput_control_lambda": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_control_lambda" + }, + "HideDatasetActionoutput_extra_files": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_extra_files" + }, + "HideDatasetActionoutput_gappedpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_gappedpeaks" + }, + "HideDatasetActionoutput_narrowpeaks": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_narrowpeaks" + }, + "HideDatasetActionoutput_summits": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_summits" + }, + "HideDatasetActionoutput_tabular": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_tabular" + }, + "HideDatasetActionoutput_treat_pileup": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_treat_pileup" + } + }, + "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_version": "2.1.0.20151222.0", + "type": "tool", + "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", + "workflow_outputs": [ + { + "label": null, + "output_name": "output_plot", + "uuid": "32ac3a7b-5509-45fe-a69e-abfd2b33f0be" + } + ] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", + "id": 9, + "input_connections": { + "infile_control": { + "id": 8, + "output_name": "output_control_lambda" + }, + "infile_treatment": { + "id": 8, + "output_name": "output_treat_pileup" + } + }, + "inputs": [], + "label": null, + "name": "MACS2 bdgcmp", + "outputs": [ + { + "name": "outfile", + "type": "bedgraph" + } + ], + "position": { + "left": 2087.5, + "top": 426.5 + }, + "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_version": "2.1.0.20151222.0", + "type": "tool", + "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", + "workflow_outputs": [ + { + "label": null, + "output_name": "outfile", + "uuid": "6b9699e0-5597-4810-9e3c-1f81149ea132" + } + ] + }, + "10": { + "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", + "content_id": "wig_to_bigWig", + "id": 10, + "input_connections": { + "input1": { + "id": 9, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Wig/BedGraph-to-bigWig", + "outputs": [ + { + "name": "out_file1", + "type": "bigwig" + } + ], + "position": { + "left": 2292.546875, + "top": 447.71875 + }, + "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_version": "1.1.0", + "type": "tool", + "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", + "workflow_outputs": [ + { + "label": null, + "output_name": "out_file1", + "uuid": "8e824df2-af08-4fa7-bba5-221044f10c1b" + } + ] + } + }, + "uuid": "bf6866e8-1ed1-4684-8dbd-fc8744257dcb" +} \ No newline at end of file
--- a/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga Fri Jul 22 14:41:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,469 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"input_file\", \"set2\": \"exp_file\"}]}", - "format-version": "0.1", - "name": "TF ChIP-Seq analysis using MACS2: danRer7", - "steps": { - "0": { - "annotation": "", - "content_id": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "exp_file" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 206, - "top": 381.265625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"exp_file\"}", - "tool_version": null, - "type": "data_input", - "uuid": "dd984d64-daac-4547-9989-9303056523d3", - "workflow_outputs": [] - }, - "1": { - "annotation": "", - "content_id": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "input_file" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 201, - "top": 516.265625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"input_file\"}", - "tool_version": null, - "type": "data_input", - "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", - "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": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "FASTQ Parallel Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 422, - "top": 341.265625 - }, - "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_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\": \"null\"}", - "tool_version": "0.3.1", - "type": "tool", - "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", - "id": 3, - "input_connections": { - "input_file": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "FASTQ Parallel Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 423, - "top": 493.265625 - }, - "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_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\": \"null\"}", - "tool_version": "0.3.1", - "type": "tool", - "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", - "workflow_outputs": [] - }, - "4": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "id": 4, - "input_connections": { - "singlePaired|sInput1": { - "id": 2, - "output_name": "output_file" - } - }, - "inputs": [], - "label": null, - "name": "Map with Bowtie for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - }, - { - "name": "output_suppressed_reads_l", - "type": "fastq" - }, - { - "name": "output_suppressed_reads_r", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_l", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_r", - "type": "fastq" - } - ], - "position": { - "left": 755.5, - "top": 272.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "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\\\": 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": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", - "workflow_outputs": [] - }, - "5": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "id": 5, - "input_connections": { - "singlePaired|sInput1": { - "id": 3, - "output_name": "output_file" - } - }, - "inputs": [], - "label": null, - "name": "Map with Bowtie for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - }, - { - "name": "output_suppressed_reads_l", - "type": "fastq" - }, - { - "name": "output_suppressed_reads_r", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_l", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_r", - "type": "fastq" - } - ], - "position": { - "left": 759.5, - "top": 492.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "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\\\": 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": "a09286be-e5ba-45fb-be1f-585fe79cf677", - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", - "id": 6, - "input_connections": { - "source|input1": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SAM-to-BAM", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 1070.5, - "top": 376.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "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\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.0", - "type": "tool", - "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", - "id": 7, - "input_connections": { - "source|input1": { - "id": 5, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SAM-to-BAM", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 1071.5, - "top": 533.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "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\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.0", - "type": "tool", - "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", - "workflow_outputs": [] - }, - "8": { - "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": { - "input_control_file": { - "id": 7, - "output_name": "output1" - }, - "input_treatment_file": { - "id": 6, - "output_name": "output1" - } - }, - "inputs": [], - "label": null, - "name": "MACS2 callpeak", - "outputs": [ - { - "name": "output_tabular", - "type": "tabular" - }, - { - "name": "output_broadpeaks", - "type": "bed" - }, - { - "name": "output_gappedpeaks", - "type": "bed" - }, - { - "name": "output_narrowpeaks", - "type": "bed" - }, - { - "name": "output_summits", - "type": "bed" - }, - { - "name": "output_plot", - "type": "pdf" - }, - { - "name": "output_treat_pileup", - "type": "bedgraph" - }, - { - "name": "output_control_lambda", - "type": "bedgraph" - }, - { - "name": "output_extra_files", - "type": "html" - } - ], - "position": { - "left": 1310.5, - "top": 358.5 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", - "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\": \"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": "e8e38d74-1a63-4c58-b042-487838e9edc7", - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "id": 9, - "input_connections": { - "infile_control": { - "id": 8, - "output_name": "output_control_lambda" - }, - "infile_treatment": { - "id": 8, - "output_name": "output_treat_pileup" - } - }, - "inputs": [], - "label": null, - "name": "MACS2 bdgcmp", - "outputs": [ - { - "name": "outfile", - "type": "bedgraph" - } - ], - "position": { - "left": 1648, - "top": 426.5 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "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\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", - "tool_version": "2.1.0.20151222.0", - "type": "tool", - "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", - "workflow_outputs": [] - }, - "10": { - "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", - "content_id": "wig_to_bigWig", - "id": 10, - "input_connections": { - "input1": { - "id": 9, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Wig/BedGraph-to-bigWig", - "outputs": [ - { - "name": "out_file1", - "type": "bigwig" - } - ], - "position": { - "left": 1853.046875, - "top": 447.71875 - }, - "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_version": "1.1.0", - "type": "tool", - "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", - "workflow_outputs": [] - } - }, - "uuid": "0838c78b-f387-440c-a3ac-c26e1f096f08" -} \ No newline at end of file
--- a/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga Fri Jul 22 14:41:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,469 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"input_file\", \"set2\": \"exp_file\"}]}", - "format-version": "0.1", - "name": "TF ChIP-Seq analysis using MACS2: hg19", - "steps": { - "0": { - "annotation": "", - "content_id": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "exp_file" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 206, - "top": 381.265625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"exp_file\"}", - "tool_version": null, - "type": "data_input", - "uuid": "dd984d64-daac-4547-9989-9303056523d3", - "workflow_outputs": [] - }, - "1": { - "annotation": "", - "content_id": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "input_file" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 201, - "top": 516.265625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"input_file\"}", - "tool_version": null, - "type": "data_input", - "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", - "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": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "FASTQ Parallel Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 422, - "top": 341.265625 - }, - "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_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\": \"null\"}", - "tool_version": "0.3.1", - "type": "tool", - "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", - "id": 3, - "input_connections": { - "input_file": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "FASTQ Parallel Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 423, - "top": 493.265625 - }, - "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_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\": \"null\"}", - "tool_version": "0.3.1", - "type": "tool", - "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", - "workflow_outputs": [] - }, - "4": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "id": 4, - "input_connections": { - "singlePaired|sInput1": { - "id": 2, - "output_name": "output_file" - } - }, - "inputs": [], - "label": null, - "name": "Map with Bowtie for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - }, - { - "name": "output_suppressed_reads_l", - "type": "fastq" - }, - { - "name": "output_suppressed_reads_r", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_l", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_r", - "type": "fastq" - } - ], - "position": { - "left": 755.5, - "top": 272.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "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\\\": \\\"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": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", - "workflow_outputs": [] - }, - "5": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "id": 5, - "input_connections": { - "singlePaired|sInput1": { - "id": 3, - "output_name": "output_file" - } - }, - "inputs": [], - "label": null, - "name": "Map with Bowtie for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - }, - { - "name": "output_suppressed_reads_l", - "type": "fastq" - }, - { - "name": "output_suppressed_reads_r", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_l", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_r", - "type": "fastq" - } - ], - "position": { - "left": 759.5, - "top": 492.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "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\\\": \\\"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": "a09286be-e5ba-45fb-be1f-585fe79cf677", - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", - "id": 6, - "input_connections": { - "source|input1": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SAM-to-BAM", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 1069.5, - "top": 376.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "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\\\": \\\"hg19full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.0", - "type": "tool", - "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", - "id": 7, - "input_connections": { - "source|input1": { - "id": 5, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SAM-to-BAM", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 1071.5, - "top": 533.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "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\\\": \\\"hg19full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.0", - "type": "tool", - "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", - "workflow_outputs": [] - }, - "8": { - "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": { - "input_control_file": { - "id": 7, - "output_name": "output1" - }, - "input_treatment_file": { - "id": 6, - "output_name": "output1" - } - }, - "inputs": [], - "label": null, - "name": "MACS2 callpeak", - "outputs": [ - { - "name": "output_tabular", - "type": "tabular" - }, - { - "name": "output_broadpeaks", - "type": "bed" - }, - { - "name": "output_gappedpeaks", - "type": "bed" - }, - { - "name": "output_narrowpeaks", - "type": "bed" - }, - { - "name": "output_summits", - "type": "bed" - }, - { - "name": "output_plot", - "type": "pdf" - }, - { - "name": "output_treat_pileup", - "type": "bedgraph" - }, - { - "name": "output_control_lambda", - "type": "bedgraph" - }, - { - "name": "output_extra_files", - "type": "html" - } - ], - "position": { - "left": 1310.5, - "top": 358.5 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", - "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\\\": \\\"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": "e8e38d74-1a63-4c58-b042-487838e9edc7", - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "id": 9, - "input_connections": { - "infile_control": { - "id": 8, - "output_name": "output_control_lambda" - }, - "infile_treatment": { - "id": 8, - "output_name": "output_treat_pileup" - } - }, - "inputs": [], - "label": null, - "name": "MACS2 bdgcmp", - "outputs": [ - { - "name": "outfile", - "type": "bedgraph" - } - ], - "position": { - "left": 1648, - "top": 426.5 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "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\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", - "tool_version": "2.1.0.20151222.0", - "type": "tool", - "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", - "workflow_outputs": [] - }, - "10": { - "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", - "content_id": "wig_to_bigWig", - "id": 10, - "input_connections": { - "input1": { - "id": 9, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Wig/BedGraph-to-bigWig", - "outputs": [ - { - "name": "out_file1", - "type": "bigwig" - } - ], - "position": { - "left": 1853.046875, - "top": 447.71875 - }, - "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_version": "1.1.0", - "type": "tool", - "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", - "workflow_outputs": [] - } - }, - "uuid": "f9305594-34b1-4189-b59f-9f217a9d9b34" -} \ No newline at end of file
--- a/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga Fri Jul 22 14:41:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,469 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"input_file\", \"set2\": \"exp_file\"}]}", - "format-version": "0.1", - "name": "TF ChIP-Seq analysis using MACS2: mm10", - "steps": { - "0": { - "annotation": "", - "content_id": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "exp_file" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 206, - "top": 381.265625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"exp_file\"}", - "tool_version": null, - "type": "data_input", - "uuid": "dd984d64-daac-4547-9989-9303056523d3", - "workflow_outputs": [] - }, - "1": { - "annotation": "", - "content_id": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "input_file" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 201, - "top": 516.265625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"input_file\"}", - "tool_version": null, - "type": "data_input", - "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", - "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": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "FASTQ Parallel Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 422, - "top": 341.265625 - }, - "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_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\": \"null\"}", - "tool_version": "0.3.1", - "type": "tool", - "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", - "id": 3, - "input_connections": { - "input_file": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "FASTQ Parallel Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 423, - "top": 493.265625 - }, - "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_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\": \"null\"}", - "tool_version": "0.3.1", - "type": "tool", - "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", - "workflow_outputs": [] - }, - "4": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "id": 4, - "input_connections": { - "singlePaired|sInput1": { - "id": 2, - "output_name": "output_file" - } - }, - "inputs": [], - "label": null, - "name": "Map with Bowtie for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - }, - { - "name": "output_suppressed_reads_l", - "type": "fastq" - }, - { - "name": "output_suppressed_reads_r", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_l", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_r", - "type": "fastq" - } - ], - "position": { - "left": 755.5, - "top": 272.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "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\\\": \\\"mm10\\\", \\\"__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": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", - "workflow_outputs": [] - }, - "5": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "id": 5, - "input_connections": { - "singlePaired|sInput1": { - "id": 3, - "output_name": "output_file" - } - }, - "inputs": [], - "label": null, - "name": "Map with Bowtie for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - }, - { - "name": "output_suppressed_reads_l", - "type": "fastq" - }, - { - "name": "output_suppressed_reads_r", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_l", - "type": "fastq" - }, - { - "name": "output_unmapped_reads_r", - "type": "fastq" - } - ], - "position": { - "left": 759.5, - "top": 492.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", - "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\\\": \\\"mm10\\\", \\\"__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": "a09286be-e5ba-45fb-be1f-585fe79cf677", - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", - "id": 6, - "input_connections": { - "source|input1": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SAM-to-BAM", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 1070.5, - "top": 376.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "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\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.0", - "type": "tool", - "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", - "id": 7, - "input_connections": { - "source|input1": { - "id": 5, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SAM-to-BAM", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 1071.5, - "top": 533.265625 - }, - "post_job_actions": {}, - "tool_errors": null, - "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\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "2.0", - "type": "tool", - "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", - "workflow_outputs": [] - }, - "8": { - "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": { - "input_control_file": { - "id": 7, - "output_name": "output1" - }, - "input_treatment_file": { - "id": 6, - "output_name": "output1" - } - }, - "inputs": [], - "label": null, - "name": "MACS2 callpeak", - "outputs": [ - { - "name": "output_tabular", - "type": "tabular" - }, - { - "name": "output_broadpeaks", - "type": "bed" - }, - { - "name": "output_gappedpeaks", - "type": "bed" - }, - { - "name": "output_narrowpeaks", - "type": "bed" - }, - { - "name": "output_summits", - "type": "bed" - }, - { - "name": "output_plot", - "type": "pdf" - }, - { - "name": "output_treat_pileup", - "type": "bedgraph" - }, - { - "name": "output_control_lambda", - "type": "bedgraph" - }, - { - "name": "output_extra_files", - "type": "html" - } - ], - "position": { - "left": 1310.5, - "top": 358.5 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", - "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\": \"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": "e8e38d74-1a63-4c58-b042-487838e9edc7", - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "id": 9, - "input_connections": { - "infile_control": { - "id": 8, - "output_name": "output_control_lambda" - }, - "infile_treatment": { - "id": 8, - "output_name": "output_treat_pileup" - } - }, - "inputs": [], - "label": null, - "name": "MACS2 bdgcmp", - "outputs": [ - { - "name": "outfile", - "type": "bedgraph" - } - ], - "position": { - "left": 1648, - "top": 426.5 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", - "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\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", - "tool_version": "2.1.0.20151222.0", - "type": "tool", - "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", - "workflow_outputs": [] - }, - "10": { - "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", - "content_id": "wig_to_bigWig", - "id": 10, - "input_connections": { - "input1": { - "id": 9, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Wig/BedGraph-to-bigWig", - "outputs": [ - { - "name": "out_file1", - "type": "bigwig" - } - ], - "position": { - "left": 1853.046875, - "top": 447.71875 - }, - "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_version": "1.1.0", - "type": "tool", - "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", - "workflow_outputs": [] - } - }, - "uuid": "39cc71c7-4bc2-4aae-8d0b-579055f1e196" -} \ No newline at end of file
--- a/repository_dependencies.xml Fri Jul 22 14:41:07 2016 -0400 +++ b/repository_dependencies.xml Tue Oct 24 16:48:56 2017 -0400 @@ -4,4 +4,5 @@ <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="d04d9f1c6791" /> <repository toolshed="toolshed.g2.bx.psu.edu" name="macs2" owner="iuc" changeset_revision="6d4babad010f" /> + <repository toolshed="toolshed.g2.bx.psu.edu" name="split_paired_collection" owner="refinery-platform" changeset_revision="3a60513b51a2" /> </repositories>