diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga index 16b443daa..7135ae293 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Get Confident Peaks From ATAC or CUTandRUN duplicates", "steps": { "0": { @@ -105,12 +105,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Line/Word/Character count", - "name": "input1" - } - ], + "inputs": [], "label": "count number of reads", "name": "Line/Word/Character count", "outputs": [ @@ -131,7 +126,7 @@ } }, "tool_id": "wc_gnu", - "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"options\": [\"lines\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "2033920a-7b40-48d1-af36-1d48be78f5df", @@ -140,7 +135,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -216,15 +211,15 @@ "output_name": "output_treat_pileup" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "640d3af5d833", + "changeset_revision": "86e2413cf3f8", "name": "macs2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": true, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": true}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"control\": {\"c_select\": \"No\", \"__current_case__\": 1}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 4, \"gsize\": {\"__class__\": \"ConnectedValue\"}}, \"format\": \"BED\", \"nomodel_type\": {\"nomodel_type_selector\": \"nomodel\", \"__current_case__\": 1, \"extsize\": \"200\", \"shift\": \"-100\"}, \"outputs\": [\"bdg\", \"peaks_tabular\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.7.1+galaxy0", + "tool_version": "2.2.9.1+galaxy0", "type": "tool", "uuid": "8f2a3aa4-704e-4d90-a672-94b97996dd56", "when": null, @@ -516,7 +511,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "errors": null, "id": 11, "input_connections": { @@ -556,15 +551,15 @@ "output_name": "outFileName" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "f6f246438eda", + "changeset_revision": "4a53856a5b85", "name": "deeptools_bigwig_average", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": {\"__class__\": \"ConnectedValue\"}, \"skipNAs\": false, \"scaleFactors\": \"1\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"bigwigs\": {\"__class__\": \"ConnectedValue\"}, \"outFileFormat\": \"bigwig\", \"region\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.5.2+galaxy0", + "tool_version": "3.5.4+galaxy0", "type": "tool", "uuid": "36059130-5f2a-4fe0-8b36-58073595fdd5", "when": null, @@ -630,12 +625,7 @@ "output_name": "integer_param" } }, - "inputs": [ - { - "description": "runtime parameter for tool Select random lines", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Select random lines", "outputs": [ @@ -650,7 +640,7 @@ }, "post_job_actions": {}, "tool_id": "random_lines1", - "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": {\"__class__\": \"ConnectedValue\"}, \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": {\"__class__\": \"ConnectedValue\"}, \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0.2", "type": "tool", "uuid": "3e8fb767-df42-47d4-b371-8ab9d0f5e26f", @@ -659,7 +649,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -717,15 +707,15 @@ "output_name": "output_treat_pileup" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "640d3af5d833", + "changeset_revision": "86e2413cf3f8", "name": "macs2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": true, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": true}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"control\": {\"c_select\": \"No\", \"__current_case__\": 1}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 4, \"gsize\": {\"__class__\": \"ConnectedValue\"}}, \"format\": \"BED\", \"nomodel_type\": {\"nomodel_type_selector\": \"nomodel\", \"__current_case__\": 1, \"extsize\": \"200\", \"shift\": \"-100\"}, \"outputs\": [\"peaks_tabular\"], \"treatment\": {\"t_multi_select\": \"Yes\", \"__current_case__\": 1, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.7.1+galaxy0", + "tool_version": "2.2.9.1+galaxy0", "type": "tool", "uuid": "e183ec20-d4ab-427a-9a0c-3e9bbced8793", "when": null, @@ -965,7 +955,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"