Mercurial > repos > rnateam > blockclust_workflow
diff blockclust_workflow.ga @ 0:b2040467dad2 draft
Uploaded
| author | rnateam |
|---|---|
| date | Tue, 06 May 2014 12:51:51 -0400 |
| parents | |
| children | 1e6d0af8c450 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blockclust_workflow.ga Tue May 06 12:51:51 2014 -0400 @@ -0,0 +1,461 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "BlockClustWorkflow", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input BAM file" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 267, + "top": 257.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input BAM file\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "tool_mode|reads_bam": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 524, + "top": 323 + }, + "post_job_actions": { + "HideDatasetActioncluster_dist": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_dist" + }, + "HideDatasetActioncluster_hclust": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_hclust" + }, + "HideDatasetActionclusters": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "clusters" + }, + "HideDatasetActionhclust_plot": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "hclust_plot" + }, + "HideDatasetActionmodel_based_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "model_based_pred_bed" + }, + "HideDatasetActionnearest_neighbour_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "nearest_neighbour_pred_bed" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "input": { + "id": 1, + "output_name": "tags_bed" + } + }, + "inputs": [], + "name": "Sort", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 797, + "top": 355 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "sort1", + "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", + "tool_version": "1.0.3", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "blockbuster", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 970, + "top": 225 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", + "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"2\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", + "tool_version": "0.1", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "tool_mode|input_bbo": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool BlockClust", + "name": "tool_mode" + } + ], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 1232, + "top": 321 + }, + "post_job_actions": { + "HideDatasetActioncluster_dist": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_dist" + }, + "HideDatasetActioncluster_hclust": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_hclust" + }, + "HideDatasetActionclusters": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "clusters" + }, + "HideDatasetActionnearest_neighbour_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "nearest_neighbour_pred_bed" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": \\\"model_based\\\", \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "clusters" + } + }, + "inputs": [], + "name": "Extract Genomic DNA", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1495, + "top": 248 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Extract genomic DNA 1", + "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", + "tool_version": "2.2.3", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "seqdb": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Search covariance model(s)", + "outputs": [ + { + "name": "outfile", + "type": "tabular" + }, + { + "name": "multiple_alignment_output", + "type": "tabular" + } + ], + "position": { + "left": 1753, + "top": 247 + }, + "post_job_actions": { + "HideDatasetActionmultiple_alignment_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "multiple_alignment_output" + }, + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2", + "tool_state": "{\"A\": \"\\\"False\\\"\", \"nohmm\": \"\\\"False\\\"\", \"--acyk\": \"\\\"False\\\"\", \"bottomonly\": \"\\\"False\\\"\", \"g\": \"\\\"False\\\"\", \"inclusion_thresholds_opts\": \"{\\\"inclusion_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"max\": \"\\\"False\\\"\", \"notrunc\": \"\\\"False\\\"\", \"mid\": \"\\\"False\\\"\", \"seqdb\": \"null\", \"toponly\": \"\\\"False\\\"\", \"cm_opts\": \"{\\\"database\\\": null, \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"cyk\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0.2", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "tool_mode|clusters_bed": { + "id": 4, + "output_name": "clusters" + }, + "tool_mode|cmsearch_out": { + "id": 6, + "output_name": "outfile" + }, + "tool_mode|sim_tab_in": { + "id": 4, + "output_name": "sim_tab_out" + } + }, + "inputs": [], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 2049, + "top": 433 + }, + "post_job_actions": { + "HideDatasetActionclusters": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "clusters" + }, + "HideDatasetActionhclust_plot": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "hclust_plot" + }, + "HideDatasetActionmodel_based_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "model_based_pred_bed" + }, + "HideDatasetActionnearest_neighbour_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "nearest_neighbour_pred_bed" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file