diff --git a/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi.ga b/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi.ga index 0f83eed6e69c50..a54b17ba6003f9 100644 --- a/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi.ga +++ b/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi.ga @@ -4,8 +4,8 @@ "creator": [ { "class": "Person", - "name": "Friederike D\u00fcndar", - "url": "https://github.com/friedue" + "identifier": "0000-0002-2301-112X", + "name": "Friederike D\u00fcndar" }, { "class": "Person", @@ -19,18 +19,18 @@ }, { "class": "Person", - "name": "Vivek Bhardwaj", - "url": "https://github.com/vivekbhr" + "identifier": "0000-0002-5570-9338", + "name": "Vivek Bhardwaj" }, { "class": "Person", - "name": "Fidel Ramirez", - "url": "https://github.com/fidelram" + "identifier": "0000-0002-9142-417X", + "name": "Fidel Ramirez" }, { "class": "Person", - "name": "Leily Rabbani", - "url": "https://github.com/LeilyR" + "identifier": "0009-0007-0755-3643", + "name": "Leily Rabbani" }, { "class": "Person", @@ -39,6 +39,7 @@ } ], "format-version": "0.1", + "license": "CC-BY-4.0", "name": "GTN - ChIP Seq - Formation Of Super Structures On Xi", "steps": { "0": { @@ -336,8 +337,8 @@ } ], "position": { - "left": 365.35189091130155, - "top": 1145.7303105939527 + "left": 365.34370837604433, + "top": 1148.1761191744758 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", @@ -348,11 +349,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"adapters\": null, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "0.73+galaxy0", "type": "tool", "uuid": "050de359-8cb9-410e-8c61-af8ab5bb0a2f", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_rep1_read2_fastqc", + "output_name": "text_file", + "uuid": "892e22b2-3194-4076-af80-357530c17186" + } + ] }, "11": { "annotation": "", @@ -399,11 +406,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"params\": {\"settingsType\": \"custom\", \"__current_case__\": 1, \"quality\": \"15\", \"stringency\": \"3\", \"error_rate\": \"0.1\", \"min_length\": \"20\", \"clip_R1\": null, \"clip_R2\": null, \"report\": true, \"retain_unpaired\": {\"retain_unpaired_select\": \"no_output\", \"__current_case__\": 0}}, \"rrbs\": {\"settingsType\": \"default\", \"__current_case__\": 0}, \"singlePaired\": {\"sPaired\": \"paired\", \"__current_case__\": 1, \"input_mate1\": {\"__class__\": \"ConnectedValue\"}, \"input_mate2\": {\"__class__\": \"ConnectedValue\"}, \"trimming\": {\"trimming_select\": \"\", \"__current_case__\": 0}, \"trim1\": false, \"three_prime_clip_R1\": null, \"three_prime_clip_R2\": null}, \"trimming\": {\"settingsType\": \"default\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "0.6.7+galaxy0", "type": "tool", "uuid": "8ba82aa7-e90d-454d-9afe-c91330d88518", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_rep1_trim_galore", + "output_name": "report_file", + "uuid": "a66a6432-690f-4e66-88c0-7eba0a014677" + } + ] }, "12": { "annotation": "", @@ -442,11 +455,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"adapters\": null, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "0.73+galaxy0", "type": "tool", "uuid": "520cd22e-8862-4b07-b156-07b50e66e3f1", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_rep1_read1_fastqc", + "output_name": "text_file", + "uuid": "da453096-fdd9-44ee-b83b-e4eca5c800f9" + } + ] }, "13": { "annotation": "", @@ -481,7 +500,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.0.4", "type": "tool", "uuid": "c9a86595-3d43-411b-a227-ba71a0a479a9", "when": null, @@ -520,7 +539,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bam\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamInput\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"25\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"exactScaling\": false, \"outFileFormat\": \"bedgraph\", \"region\": \"chrX\", \"scaling\": {\"type\": \"1x\", \"__current_case__\": 4, \"effectiveGenomeSize\": {\"effectiveGenomeSize_opt\": \"2308125349\", \"__current_case__\": 7}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "f2f39152-9f70-4798-89ee-ccd389c51082", "when": null, @@ -559,7 +578,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bam\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamInput\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"25\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"type\": \"1x\", \"__current_case__\": 4, \"effectiveGenomeSize\": {\"effectiveGenomeSize_opt\": \"2308125349\", \"__current_case__\": 7}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "c171aad0-cb84-44e8-aac8-a289b8d8c1e5", "when": null, @@ -598,11 +617,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bam\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamInput\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"25\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"exactScaling\": false, \"outFileFormat\": \"bedgraph\", \"region\": \"chrX\", \"scaling\": {\"type\": \"1x\", \"__current_case__\": 4, \"effectiveGenomeSize\": {\"effectiveGenomeSize_opt\": \"2308125349\", \"__current_case__\": 7}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "8f239db8-258c-4c7e-85ae-4b9732665c4a", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_rep1_bamcoverage", + "output_name": "outFileName", + "uuid": "73e2f018-d9e4-4f74-8110-598b9b43a940" + } + ] }, "17": { "annotation": "", @@ -637,11 +662,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.0.4", "type": "tool", "uuid": "8377fd06-d480-42ee-a677-5fd05d73083e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_rep1_idxstats", + "output_name": "output", + "uuid": "09449d6f-ce88-4448-9928-064c729c32d1" + } + ] }, "18": { "annotation": "", @@ -651,11 +682,11 @@ "input_connections": { "multibam_conditional|bamfiles": [ { - "id": 2, + "id": 3, "output_name": "output" }, { - "id": 3, + "id": 2, "output_name": "output" } ] @@ -682,7 +713,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": \"500\", \"numberOfSamples\": \"10000\", \"doExtendCustom\": {\"doExtend\": \"no\", \"__current_case__\": 0}, \"ignoreDuplicates\": false, \"centerReads\": false, \"minMappingQuality\": \"1\", \"samFlagInclude\": null, \"samFlagExclude\": null, \"minFragmentLength\": \"0\", \"maxFragmentLength\": \"0\", \"skipZeros\": false, \"plotTitle\": \"\", \"blackListFileName\": null}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"multibam_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bamfiles\": {\"__class__\": \"ConnectedValue\"}}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"region\": \"chrX\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "d05f9875-4f36-4ba6-ada4-f58db54b6589", "when": null, @@ -733,7 +764,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "e90eeeda-e9b6-49a3-b148-2f4bd61bce7f", "when": null, @@ -780,11 +811,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": false, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": false}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"control\": {\"c_select\": \"Yes\", \"__current_case__\": 0, \"c_multiple\": {\"c_multi_select\": \"No\", \"__current_case__\": 0, \"input_control_file\": {\"__class__\": \"ConnectedValue\"}}}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"1870000000\", \"__current_case__\": 1}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.2.7.1+galaxy0", "type": "tool", "uuid": "09aaf86a-b1ce-4f03-8191-5f2b1c52da8e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_input_rep1_macs2", + "output_name": "output_narrowpeaks", + "uuid": "a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd" + } + ] }, "21": { "annotation": "", @@ -823,11 +860,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bedgraph\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "f250f272-26ab-4af8-a34a-a7b2e810773c", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_input_rep1_bamcompare", + "output_name": "outFileName", + "uuid": "5174d1aa-21f6-4187-8935-70ba8bd0f6e0" + } + ] }, "22": { "annotation": "", @@ -874,7 +917,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "ac7ce980-870d-4e3b-8e55-dc85e507655b", "when": null, @@ -921,7 +964,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": false, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": false}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"control\": {\"c_select\": \"Yes\", \"__current_case__\": 0, \"c_multiple\": {\"c_multi_select\": \"No\", \"__current_case__\": 0, \"input_control_file\": {\"__class__\": \"ConnectedValue\"}}}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"1870000000\", \"__current_case__\": 1}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.2.7.1+galaxy0", "type": "tool", "uuid": "a358caee-9660-4798-be68-49773d3fce96", "when": null, @@ -964,7 +1007,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bedgraph\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "365193ec-fb99-489b-9588-ad88f4ab96ff", "when": null, @@ -985,16 +1028,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool bamCompare", - "name": "bamFile1" - }, - { - "description": "runtime parameter for tool bamCompare", - "name": "bamFile2" - } - ], + "inputs": [], "label": null, "name": "bamCompare", "outputs": [ @@ -1023,8 +1057,8 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"RuntimeValue\"}, \"bamFile2\": {\"__class__\": \"RuntimeValue\"}, \"binSize\": \"50\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "b7f0fd5c-25cd-49b6-b7de-3b6dfddcb375", "when": null, @@ -1071,7 +1105,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": false, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": false}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"control\": {\"c_select\": \"Yes\", \"__current_case__\": 0, \"c_multiple\": {\"c_multi_select\": \"No\", \"__current_case__\": 0, \"input_control_file\": {\"__class__\": \"ConnectedValue\"}}}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"1870000000\", \"__current_case__\": 1}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.2.7.1+galaxy0", "type": "tool", "uuid": "83c717f5-d44e-4b89-8729-9ce3f5ada959", "when": null, @@ -1122,7 +1156,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bam\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "cc54d7da-d1c8-4d3f-a676-4a906fef0895", "when": null, @@ -1169,7 +1203,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": false, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": false}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"control\": {\"c_select\": \"Yes\", \"__current_case__\": 0, \"c_multiple\": {\"c_multi_select\": \"No\", \"__current_case__\": 0, \"input_control_file\": {\"__class__\": \"ConnectedValue\"}}}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"1870000000\", \"__current_case__\": 1}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.2.7.1+galaxy0", "type": "tool", "uuid": "763d8b18-e31e-49dd-b124-c209e47d8a65", "when": null, @@ -1220,7 +1254,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bam\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "05d06db5-4168-4967-971d-b23bbdc52d1f", "when": null, @@ -1267,7 +1301,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": false, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": false}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"control\": {\"c_select\": \"Yes\", \"__current_case__\": 0, \"c_multiple\": {\"c_multi_select\": \"No\", \"__current_case__\": 0, \"input_control_file\": {\"__class__\": \"ConnectedValue\"}}}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"1870000000\", \"__current_case__\": 1}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.2.7.1+galaxy0", "type": "tool", "uuid": "df4404af-2dc7-44cb-9206-f6f46d3ab612", "when": null, @@ -1336,7 +1370,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bam\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"modeOpt\": \"bins\", \"__current_case__\": 0, \"binSize\": \"1000\", \"distanceBetweenBins\": \"500\"}, \"multibam_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bamfiles\": {\"__class__\": \"ConnectedValue\"}}, \"outRawCounts\": false, \"region\": \"chrX\", \"scalingFactors\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "1ec767b6-72b9-4b3a-9dbd-37f5130161c8", "when": null, @@ -1387,7 +1421,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bam\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"bamFile1\": {\"__class__\": \"ConnectedValue\"}, \"bamFile2\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"50\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"comparison\": {\"type\": \"log2\", \"__current_case__\": 0, \"pseudocount\": \"1 1\"}, \"exactScaling\": false, \"outFileFormat\": \"bigwig\", \"region\": \"chrX\", \"scaling\": {\"method\": \"readCount\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "11f2a819-d11f-44dd-a948-268848295bc9", "when": null, @@ -1434,7 +1468,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": false, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": false}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"control\": {\"c_select\": \"Yes\", \"__current_case__\": 0, \"c_multiple\": {\"c_multi_select\": \"No\", \"__current_case__\": 0, \"input_control_file\": {\"__class__\": \"ConnectedValue\"}}}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"1870000000\", \"__current_case__\": 1}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.2.7.1+galaxy0", "type": "tool", "uuid": "1dd53065-e792-48d9-9a34-e462746e18b2", "when": null, @@ -1481,11 +1515,17 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": \"mm10\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.5.0+galaxy0", "type": "tool", "uuid": "9dfaa574-93d3-49ab-a194-4ed47017918a", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_rep1_bowtie2", + "output_name": "mapping_stats", + "uuid": "4c3ca5b1-2298-4bb4-8d2f-f62619f35158" + } + ] }, "35": { "annotation": "", @@ -1518,7 +1558,7 @@ "post_job_actions": {}, "tool_id": "cat1", "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "1.0.0", "type": "tool", "uuid": "93e86b36-c41d-4f6e-aa0d-f44fc54e1bcf", "when": null, @@ -1557,7 +1597,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"corData\": {\"__class__\": \"ConnectedValue\"}, \"corMethod\": \"pearson\", \"outFileCorMatrix\": false, \"outFileFormat\": \"png\", \"plotting_type\": {\"whatToPlot\": \"heatmap\", \"__current_case__\": 0, \"zMin\": \"\", \"zMax\": \"\", \"colorMap\": \"RdYlBu\", \"plotTitle\": \"\", \"plotNumbers\": false, \"plotHeight\": \"9.5\", \"plotWidth\": \"11.0\"}, \"removeOutliers\": false, \"skipZeros\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "6e724d39-d914-4e3b-9981-f7f87434bade", "when": null, @@ -1610,7 +1650,7 @@ "post_job_actions": {}, "tool_id": "cat1", "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input2\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input2\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"input2\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 4, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "1.0.0", "type": "tool", "uuid": "b6e36905-ee81-4ea9-bfd0-b0748447a0f4", "when": null, @@ -1649,7 +1689,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"genome_file_opts\": {\"genome_file_opts_selector\": \"loc\", \"__current_case__\": 0, \"genome\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.30.0+galaxy2", "type": "tool", "uuid": "862416d4-227b-4f67-92d7-8b8078d04151", "when": null, @@ -1688,7 +1728,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"genome_file_opts\": {\"genome_file_opts_selector\": \"loc\", \"__current_case__\": 0, \"genome\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.30.0+galaxy2", "type": "tool", "uuid": "c6b88816-2161-4b9a-8cc7-1435ce7d83c8", "when": null, @@ -1721,17 +1761,23 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "fe5b4cb8356c", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bed\", \"c_and_o_argument_repeat\": [], \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"distance\": \"0\", \"header\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.30.0", "type": "tool", "uuid": "944931ba-824d-4976-9990-a3b64b607dca", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_H3K4me3_CTCF_rep1_mergebed", + "output_name": "output", + "uuid": "931eb26a-0e5d-4556-b67f-1c37372aaf28" + } + ] }, "41": { "annotation": "", @@ -1760,17 +1806,23 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "fe5b4cb8356c", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bed\", \"c_and_o_argument_repeat\": [], \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"distance\": \"0\", \"header\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "2.30.0", "type": "tool", "uuid": "b3c82d22-9c6b-4f18-91bf-6a33132232ce", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "wt_all_mergebed", + "output_name": "output", + "uuid": "9c4c5a1f-f2c1-4e83-b1f9-ff32ee48baeb" + } + ] }, "42": { "annotation": "", @@ -1815,7 +1867,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bed\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"mode_select\": \"reference-point\", \"__current_case__\": 1, \"referencePoint\": \"center\", \"nanAfterEnd\": false, \"beforeRegionStartLength\": \"3000\", \"afterRegionStartLength\": \"3000\"}, \"multibigwig_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bigwigfiles\": {\"__class__\": \"ConnectedValue\"}}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"regionsFiles\": [{\"__index__\": 0, \"regionsFile\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "79d2ee45-1b6e-4c31-b75c-beb7d0b80831", "when": null, @@ -1880,7 +1932,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"bed\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"mode_select\": \"reference-point\", \"__current_case__\": 1, \"referencePoint\": \"center\", \"nanAfterEnd\": false, \"beforeRegionStartLength\": \"3000\", \"afterRegionStartLength\": \"3000\"}, \"multibigwig_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bigwigfiles\": {\"__class__\": \"ConnectedValue\"}}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"regionsFiles\": [{\"__index__\": 0, \"regionsFile\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.0", "type": "tool", "uuid": "c32eccc5-ece8-4d91-85fc-f8d1ba9cc2ff", "when": null, @@ -1919,7 +1971,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"sortRegions\": \"descend\", \"sortUsing\": \"mean\", \"sortUsingSamples\": null, \"linesAtTickMarks\": false, \"averageTypeSummaryPlot\": \"mean\", \"plotType\": \"lines\", \"missingDataColor\": \"black\", \"colorMapRepeat\": [], \"alpha\": \"1.0\", \"colorList\": \"\", \"zMin\": \"\", \"zMax\": \"\", \"yMin\": null, \"yMax\": null, \"xAxisLabel\": \"distance from TSS (bp)\", \"yAxisLabel\": \"genes\", \"heatmapWidth\": \"7.5\", \"heatmapHeight\": \"25.0\", \"whatToShow\": \"plot, heatmap and colorbar\", \"startLabel\": \"TSS\", \"endLabel\": \"TES\", \"referencePointLabel\": \"TSS\", \"samplesLabel\": null, \"regionsLabel\": null, \"plotTitle\": \"\", \"legendLocation\": \"best\", \"labelRotation\": \"0\", \"perGroup\": false, \"used_multiple_regions\": {\"used_multiple_regions_options\": \"no\", \"__current_case__\": 0, \"clustering\": {\"clustering_options\": \"kmeans\", \"__current_case__\": 0, \"k_kmeans\": \"2\"}, \"silhouette\": false}, \"clusterUsingSamples\": null}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"matrixFile\": {\"__class__\": \"ConnectedValue\"}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.1", "type": "tool", "uuid": "938daaba-fe5d-4a17-935c-0e34d30757c5", "when": null, @@ -1958,7 +2010,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"sortRegions\": \"descend\", \"sortUsing\": \"mean\", \"sortUsingSamples\": null, \"linesAtTickMarks\": false, \"averageTypeSummaryPlot\": \"mean\", \"plotType\": \"lines\", \"missingDataColor\": \"black\", \"colorMapRepeat\": [], \"alpha\": \"1.0\", \"colorList\": \"\", \"zMin\": \"\", \"zMax\": \"\", \"yMin\": null, \"yMax\": null, \"xAxisLabel\": \"distance from TSS (bp)\", \"yAxisLabel\": \"genes\", \"heatmapWidth\": \"7.5\", \"heatmapHeight\": \"25.0\", \"whatToShow\": \"plot, heatmap and colorbar\", \"startLabel\": \"\", \"endLabel\": \"\", \"referencePointLabel\": \"\", \"samplesLabel\": null, \"regionsLabel\": null, \"plotTitle\": \"\", \"legendLocation\": \"best\", \"labelRotation\": \"0\", \"perGroup\": false, \"used_multiple_regions\": {\"used_multiple_regions_options\": \"no\", \"__current_case__\": 0, \"clustering\": {\"clustering_options\": \"kmeans\", \"__current_case__\": 0, \"k_kmeans\": \"6\"}, \"silhouette\": false}, \"clusterUsingSamples\": null}, \"matrixFile\": {\"__class__\": \"ConnectedValue\"}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "3.5.1.0.1", "type": "tool", "uuid": "3474931f-6d25-46ea-91d0-19c1e89d4626", "when": null, @@ -1968,6 +2020,6 @@ "tags": [ "epigenetics" ], - "uuid": "1a256d36-4c30-4b42-bb97-a6ed4d6b1224", - "version": 6 + "uuid": "99992a6e-8e4f-4ee3-b91c-e9671747d337", + "version": 10 } \ No newline at end of file