GraphClust_main_3r.ga

{"uuid": "bfc62aa5-bee2-4aa6-8c97-1f82e8dd8db3", "tags": [], "format-version": "0.1", "name": "GraphClust_main_3r", "version": 1, "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "ef587dc1-2d30-491e-927d-5a3569e8176f", "label": null}], "input_connections": {}, "tool_state": "{\"name\": \"Input Dataset\"}", "id": 0, "uuid": "60988a8d-a50c-45f6-89bb-14ec5adbb83c", "errors": null, "name": "Input dataset", "label": null, "inputs": [{"name": "Input Dataset", "description": ""}], "position": {"top": 278.9423141479492, "left": 200}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.5", "tool_version": "0.5", "outputs": [{"type": "fasta", "name": "data.fasta"}, {"type": "txt", "name": "data.map"}, {"type": "txt", "name": "data.names"}, {"type": "fasta", "name": "data.fasta.scan"}, {"type": "zip", "name": "FASTA"}, {"type": "txt", "name": "shape_data_split"}, {"type": "stockholm", "name": "alignment_data_split"}], "workflow_outputs": [], "input_connections": {"fastaFile": {"output_name": "output", "id": 0}}, "tool_state": "{\"fastaFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"in_winShift\": \"\\\"70\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"min_seq_length\": \"\\\"5\\\"\", \"max_length\": \"\\\"250\\\"\", \"AlignmentData\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"SHAPEdata\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 1, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "2a5defc09381", "name": "graphclust_preprocessing", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "79ef5ef7-060f-4e74-9a10-9ad39df51b7d", "errors": null, "name": "Preprocessing", "post_job_actions": {"HideDatasetActiondata.names": {"output_name": "data.names", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionalignment_data_split": {"output_name": "alignment_data_split", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionFASTA": {"output_name": "FASTA", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionshape_data_split": {"output_name": "shape_data_split", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiondata.fasta.scan": {"output_name": "data.fasta.scan", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiondata.map": {"output_name": "data.map", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiondata.fasta": {"output_name": "data.fasta", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [{"name": "AlignmentData", "description": "runtime parameter for tool Preprocessing"}, {"name": "SHAPEdata", "description": "runtime parameter for tool Preprocessing"}], "position": {"top": 261.9110641479492, "left": 409.9638671875}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.5", "type": "tool"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4", "tool_version": "2.2.10.4", "outputs": [{"type": "input", "name": "structure_outputs"}, {"type": "input", "name": "matrix_outputs"}, {"type": "dbn", "name": "dot_bracket_stdout"}], "workflow_outputs": [{"output_name": "dot_bracket_stdout", "uuid": "36752fa8-7c5e-4a8f-90c3-586d7462502a", "label": null}, {"output_name": "structure_outputs", "uuid": "c20b321f-8849-40bf-b231-c18f7483291d", "label": null}], "input_connections": {"input_source|fasta_input": {"output_name": "data.fasta", "id": 1}}, "tool_state": "{\"__page__\": null, \"mea\": \"\\\"false\\\"\", \"temperature\": \"\\\"37.0\\\"\", \"dangling\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"IDs\": \"{\\\"auto_id\\\": \\\"false\\\", \\\"id_digits\\\": \\\"4\\\", \\\"id_prefix\\\": \\\"sequence\\\", \\\"id_start\\\": \\\"1\\\"}\", \"pf\": \"\\\"false\\\"\", \"meagamma\": \"\\\"\\\"\", \"input_source\": \"{\\\"__current_case__\\\": 0, \\\"fasta_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"select_fasta\\\": \\\"true\\\"}\", \"layout_type\": \"\\\"1\\\"\", \"advancedOptions\": \"{\\\"betaScale\\\": \\\"1.0\\\", \\\"bppmThreshold\\\": \\\"1e-05\\\", \\\"circular\\\": \\\"false\\\", \\\"gquad\\\": \\\"false\\\", \\\"noclosinggu\\\": \\\"true\\\", \\\"noconversion\\\": \\\"true\\\", \\\"nogu\\\": \\\"true\\\", \\\"nolp\\\": \\\"true\\\", \\\"nops\\\": \\\"false\\\", \\\"notetra\\\": \\\"true\\\", \\\"nsp\\\": \\\"\\\"}\", \"constraints\": \"{\\\"constraintLocation\\\": {\\\"__current_case__\\\": 0, \\\"constraintSelector\\\": \\\"none\\\"}, \\\"maxBPspan\\\": \\\"-1\\\", \\\"motif\\\": \\\"\\\", \\\"shapeOption\\\": {\\\"__current_case__\\\": 1, \\\"shapeSelector\\\": \\\"notUsed\\\"}}\", \"pfscale\": \"\\\"1.07\\\"\"}", "id": 2, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "bdb786715d28", "name": "viennarna_rnafold", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "f1974a47-cbbb-4123-bf05-219bfc58f0bc", "errors": null, "name": "RNAfold", "post_job_actions": {"HideDatasetActionmatrix_outputs": {"output_name": "matrix_outputs", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 221.9711570739746, "left": 739.00244140625}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4", "type": "tool"}, "3": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.4", "tool_version": "0.4", "outputs": [{"type": "input", "name": "gspan_compressed"}], "workflow_outputs": [], "input_connections": {"dataFile": {"output_name": "dot_bracket_stdout", "id": 2}}, "tool_state": "{\"__page__\": null, \"dataFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"group\": \"\\\"10000\\\"\", \"inputFormat\": \"\\\"vrna-simple\\\"\", \"__rerun_remap_job_id__\": null, \"structureType\": \"\\\"MFE\\\"\", \"abstr\": \"\\\"false\\\"\", \"stack\": \"\\\"true\\\"\", \"seq_graph_t\": \"\\\"true\\\"\"}", "id": 3, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "d34ab3aa1724", "name": "structure_to_gspan", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "3a6bb48b-229e-4944-92e9-693f89a2fb10", "errors": null, "name": "Structure to GSPAN", "post_job_actions": {"HideDatasetActiongspan_compressed": {"output_name": "gspan_compressed", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 995.99755859375}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.4", "type": "tool"}, "4": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.3", "tool_version": "9.2.3", "outputs": [{"type": "zip", "name": "data_svector"}], "workflow_outputs": [{"output_name": "data_svector", "uuid": "34e4563b-7304-48f7-b2e0-1c4f696eb652", "label": null}], "input_connections": {"data_fasta": {"output_name": "data.fasta", "id": 1}, "gspan_file": {"output_name": "gspan_compressed", "id": 3}}, "tool_state": "{\"max_dist_relations\": \"\\\"3\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"gspan_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"data_fasta\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"max_rad\": \"\\\"3\\\"\"}", "id": 4, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "1b142e88d068", "name": "graphclust_nspdk", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "499a43b5-bbad-4f9c-a279-ca31617dddac", "errors": null, "name": "NSPDK_sparseVect", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 1324.00244140625}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.3", "type": "tool"}, "5": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3.1", "tool_version": "9.2.3.1", "outputs": [{"type": "txt", "name": "fast_cluster"}, {"type": "txt", "name": "fast_cluster_sim"}, {"type": "txt", "name": "black_list"}, {"type": "txt", "name": "fast_cluster_m"}, {"type": "txt", "name": "fast_cluster_sim_m"}, {"type": "txt", "name": "black_list_m"}], "workflow_outputs": [{"output_name": "fast_cluster", "uuid": "beaf57e9-d0dd-45da-944a-306ea2d9cb13", "label": null}], "input_connections": {"data_svector": {"output_name": "data_svector", "id": 4}, "data_fasta": {"output_name": "data.fasta", "id": 1}, "data_names": {"output_name": "data.names", "id": 1}}, "tool_state": "{\"knn\": \"\\\"10\\\"\", \"max_dist_relations\": \"\\\"3\\\"\", \"nhf\": \"\\\"500\\\"\", \"noCache\": \"\\\"true\\\"\", \"__page__\": null, \"usn\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"oc\": \"\\\"true\\\"\", \"iteration_num\": \"{\\\"CI\\\": \\\"1\\\", \\\"__current_case__\\\": 1, \\\"iteration_num_selector\\\": \\\"false\\\"}\", \"ensf\": \"\\\"5\\\"\", \"data_fasta\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"max_rad\": \"\\\"3\\\"\", \"data_svector\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"nspdk_nhf_max\": \"\\\"1000\\\"\", \"nspdk_nhf_step\": \"\\\"25\\\"\", \"GLOBAL_num_clusters\": \"\\\"100\\\"\", \"data_names\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", "id": 5, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "1b142e88d068", "name": "graphclust_nspdk", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "23071e28-0235-4860-ac22-866e000ef9b6", "errors": null, "name": "NSPDK_candidateClusters", "post_job_actions": {"HideDatasetActionfast_cluster_sim_m": {"output_name": "fast_cluster_sim_m", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfast_cluster_m": {"output_name": "fast_cluster_m", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionblack_list": {"output_name": "black_list", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfast_cluster_sim": {"output_name": "fast_cluster_sim", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionblack_list_m": {"output_name": "black_list_m", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 281.9711608886719, "left": 1570.9736328125}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3.1", "type": "tool"}, "6": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4", "tool_version": "0.4", "outputs": [{"type": "input", "name": "centers"}, {"type": "input", "name": "trees"}, {"type": "input", "name": "cmFa"}, {"type": "input", "name": "model_tree_fa"}, {"type": "input", "name": "tree_matrix"}], "workflow_outputs": [], "input_connections": {"fasta_data": {"output_name": "data.fasta", "id": 1}, "fast_cluster_sim": {"output_name": "fast_cluster_sim", "id": 5}, "data_map": {"output_name": "data.map", "id": 1}, "fast_cluster": {"output_name": "fast_cluster", "id": 5}}, "tool_state": "{\"knn\": \"\\\"10\\\"\", \"__page__\": null, \"CI\": \"\\\"1\\\"\", \"fasta_data\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"fast_cluster_sim\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"data_map\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"fast_cluster\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", "id": 6, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "5c92a3f7b59c", "name": "graphclust_prepocessing_for_mlocarna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "6969f72c-854b-4115-96fb-4279cb62c945", "errors": null, "name": "pgma_graphclust", "post_job_actions": {"HideDatasetActioncmFa": {"output_name": "cmFa", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiontrees": {"output_name": "trees", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActioncenters": {"output_name": "centers", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiontree_matrix": {"output_name": "tree_matrix", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionmodel_tree_fa": {"output_name": "model_tree_fa", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 1853.0048828125}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4", "type": "tool"}, "7": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4", "tool_version": "0.4", "outputs": [{"type": "stockholm", "name": "model_tree_stk"}], "workflow_outputs": [{"output_name": "model_tree_stk", "uuid": "08dc1dbf-89fb-48be-a28e-351ad9fc2dab", "label": null}], "input_connections": {"tree_file": {"output_name": "trees", "id": 6}, "data_map": {"output_name": "data.map", "id": 1}, "center_fa_file": {"output_name": "centers", "id": 6}, "tree_matrix": {"output_name": "tree_matrix", "id": 6}}, "tool_state": "{\"tau\": \"\\\"50\\\"\", \"max_diff_am\": \"\\\"50\\\"\", \"center_fa_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"free_endgaps\": \"\\\"0\\\"\", \"tree_matrix\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"p\": \"\\\"0.001\\\"\", \"allow_overlap\": \"\\\"false\\\"\", \"data_map\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"param_type\": \"{\\\"__current_case__\\\": 0, \\\"alifold_consensus_dp\\\": \\\"true\\\", \\\"indel\\\": \\\"-200\\\", \\\"indel_opening\\\": \\\"-400\\\", \\\"max_diff\\\": \\\"100\\\", \\\"max_diff_am\\\": \\\"50\\\", \\\"p\\\": \\\"0.001\\\", \\\"param_type_selector\\\": \\\"gclust\\\", \\\"plfold_minlen\\\": \\\"210\\\", \\\"plfold_span\\\": \\\"150\\\", \\\"plfold_winsize\\\": \\\"300\\\", \\\"struct_weight\\\": \\\"180\\\", \\\"tau\\\": \\\"50\\\"}\", \"max_diff\": \"\\\"100\\\"\", \"tree_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"plfold_minlen\": \"\\\"210\\\"\"}", "id": 7, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "c45eef4517d9", "name": "graphclust_mlocarna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "1375a903-a580-42e8-aa30-d55f6875f058", "errors": null, "name": "locarna_graphclust", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 279.9399108886719, "left": 2084.00244140625}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4", "type": "tool"}, "8": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4", "tool_version": "0.4", "outputs": [{"type": "stockholm", "name": "model_cmfinder_stk"}], "workflow_outputs": [{"output_name": "model_cmfinder_stk", "uuid": "ee4fa4a6-5fbf-4fc4-ba97-08c4a10a6118", "label": null}], "input_connections": {"model_tree_stk": {"output_name": "model_tree_stk", "id": 7}, "cmfinder_fa": {"output_name": "cmFa", "id": 6}}, "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cmfinder_fa\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"model_tree_stk\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"gap_threshold_opts\": \"{\\\"__current_case__\\\": 0, \\\"gap\\\": \\\"1.0\\\", \\\"gap_threshold_opts_selector\\\": \\\"--g\\\"}\"}", "id": 8, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "5a1dcc77b0ce", "name": "graphclust_cmfinder", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "c322fe97-43ee-4f48-8814-57919ced35a0", "errors": null, "name": "cmfinder", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 2345.9736328125}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4", "type": "tool"}, "9": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0", "tool_version": "1.1.2.0", "outputs": [{"type": "text", "name": "summary_outfile"}, {"type": "cm", "name": "cmfile_outfile"}, {"type": "stockholm", "name": "refined_multiple_alignment_output"}, {"type": "txt", "name": "hfile"}, {"type": "txt", "name": "sfile"}, {"type": "txt", "name": "qqfile"}, {"type": "txt", "name": "ffile"}, {"type": "txt", "name": "xfile"}], "workflow_outputs": [{"output_name": "cmfile_outfile", "uuid": "e35cd3cc-b278-4a5a-9400-6174b0528e5e", "label": null}], "input_connections": {"alignment_infile": {"output_name": "model_cmfinder_stk", "id": 8}}, "tool_state": "{\"__page__\": null, \"controlling_filter_p7_hmm\": \"{\\\"EgfN\\\": \\\"200\\\", \\\"ElfN\\\": \\\"200\\\", \\\"EmN\\\": \\\"200\\\", \\\"EvN\\\": \\\"200\\\", \\\"p7ere\\\": \\\"0.38\\\", \\\"p7ml\\\": \\\"false\\\"}\", \"noss\": \"\\\"false\\\"\", \"is_summery_output\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"effective_opts\": \"{\\\"__current_case__\\\": 0, \\\"effective_opts_selector\\\": \\\"--enone\\\"}\", \"alignment_infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"refining_opts\": \"{\\\"__current_case__\\\": 0, \\\"refining_opts_selector\\\": \\\"\\\"}\", \"Calibrate\": \"{\\\"L\\\": \\\"0.5\\\", \\\"__current_case__\\\": 1, \\\"add_opts\\\": {\\\"beta\\\": \\\"1e-15\\\", \\\"gc\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"nonbanded\\\": \\\"false\\\", \\\"nonull3\\\": \\\"false\\\", \\\"random\\\": \\\"false\\\", \\\"seed\\\": \\\"181\\\"}, \\\"cont_exp_tails_fits\\\": {\\\"__current_case__\\\": 0, \\\"gtailn\\\": \\\"250\\\", \\\"ltailn\\\": \\\"750\\\", \\\"selector\\\": \\\"top_n\\\"}, \\\"output_options_cond\\\": {\\\"__current_case__\\\": 1, \\\"selector\\\": \\\"none\\\"}, \\\"selector\\\": \\\"true\\\"}\", \"model_construction_opts\": \"{\\\"__current_case__\\\": 0, \\\"model_construction_opts_selector\\\": \\\"--fast\\\", \\\"symfrac\\\": \\\"0.5\\\"}\", \"relative_weights_opts\": \"{\\\"__current_case__\\\": 0, \\\"relative_weights_opts_selector\\\": \\\"--wpb\\\"}\"}", "id": 9, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "477d829d3250", "name": "infernal", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "2be13350-048f-46fd-810c-28e1fe64b03d", "errors": null, "name": "cmbuild", "post_job_actions": {"HideDatasetActionsummary_outfile": {"output_name": "summary_outfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionrefined_multiple_alignment_output": {"output_name": "refined_multiple_alignment_output", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionffile": {"output_name": "ffile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionqqfile": {"output_name": "qqfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionxfile": {"output_name": "xfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionsfile": {"output_name": "sfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionhfile": {"output_name": "hfile", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 2633.990234375}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0", "type": "tool"}, "10": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0", "tool_version": "1.1.2.0", "outputs": [{"type": "tabular", "name": "outfile"}, {"type": "tabular", "name": "multiple_alignment_output"}], "workflow_outputs": [{"output_name": "outfile", "uuid": "304599bc-a351-4e5c-b4c1-053039f5657d", "label": null}], "input_connections": {"cm_opts|cmfile": {"output_name": "cmfile_outfile", "id": 9}, "seqdb": {"output_name": "data.fasta.scan", "id": 1}}, "tool_state": "{\"anytrunc\": \"\\\"false\\\"\", \"verbose\": \"\\\"false\\\"\", \"notrunc\": \"\\\"false\\\"\", \"smxsize\": \"\\\"128.0\\\"\", \"cm_opts\": \"{\\\"__current_case__\\\": 1, \\\"cm_opts_selector\\\": \\\"histdb\\\", \\\"cmfile\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"__page__\": null, \"bottomonly\": \"\\\"false\\\"\", \"seqdb\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"inclusion_thresholds_opts\": \"{\\\"__current_case__\\\": 0, \\\"inclusion_thresholds_selector\\\": \\\"\\\"}\", \"__rerun_remap_job_id__\": null, \"mxsize\": \"\\\"128.0\\\"\", \"A\": \"\\\"false\\\"\", \"acyk\": \"\\\"false\\\"\", \"acceleration_huristics\": \"{\\\"__current_case__\\\": 1, \\\"acceleration_huristics_selector\\\": \\\"--nohmm\\\"}\", \"reporting_thresholds_opts\": \"{\\\"__current_case__\\\": 0, \\\"reporting_thresholds_selector\\\": \\\"\\\"}\", \"cyk\": \"\\\"false\\\"\", \"Z\": \"\\\"\\\"\", \"model_thresholds\": \"{\\\"cut_ga\\\": \\\"false\\\", \\\"cut_nc\\\": \\\"false\\\", \\\"cut_tc\\\": \\\"false\\\"}\", \"g\": \"\\\"true\\\"\", \"nonull3\": \"\\\"false\\\"\", \"toponly\": \"\\\"true\\\"\", \"noali\": \"\\\"false\\\"\"}", "id": 10, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "477d829d3250", "name": "infernal", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "edf3f980-3caf-494f-a90b-36ae77265706", "errors": null, "name": "cmsearch", "post_job_actions": {"HideDatasetActionmultiple_alignment_output": {"output_name": "multiple_alignment_output", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 2961.958984375}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0", "type": "tool"}, "11": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5", "tool_version": "0.5", "outputs": [{"type": "input", "name": "clusters"}, {"type": "input", "name": "allFasta"}, {"type": "input", "name": "partitions"}, {"type": "input", "name": "topSecondaryStruct"}, {"type": "input", "name": "topDot"}, {"type": "input", "name": "rscapePlot"}, {"type": "txt", "name": "final_stats"}, {"type": "tabular", "name": "tableForEval"}, {"type": "txt", "name": "final_soft"}, {"type": "txt", "name": "final_used_cmsearch"}, {"type": "txt", "name": "evaluation"}, {"type": "txt", "name": "combined_cm_out"}, {"type": "zip", "name": "RESULTS_zip"}], "workflow_outputs": [{"output_name": "topDot", "uuid": "cb238a4d-918a-429d-956d-cd490c3cfdbb", "label": null}, {"output_name": "allFasta", "uuid": "40b15d42-a115-4489-b734-e0ff23c7660a", "label": null}, {"output_name": "rscapePlot", "uuid": "4581c90c-7d1f-4885-8e02-766a8c6742e8", "label": null}, {"output_name": "topSecondaryStruct", "uuid": "6f98c498-72fd-4b38-9bda-409918253bd9", "label": null}, {"output_name": "clusters", "uuid": "1abbd49e-0c1d-4480-9595-471bd70b8210", "label": null}, {"output_name": "RESULTS_zip", "uuid": "99e54301-4b54-49f3-a440-f84749bc4b4e", "label": null}], "input_connections": {"model_tree_files": {"output_name": "model_tree_fa", "id": 6}, "FASTA": {"output_name": "FASTA", "id": 1}, "cmsearch_results": {"output_name": "outfile", "id": 10}}, "tool_state": "{\"__page__\": 0, \"model_tree_files\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cm_max_eval\": \"\\\"0.001\\\"\", \"min_cluster_size\": \"\\\"3\\\"\", \"advanced_opts\": \"{\\\"__current_case__\\\": 1, \\\"advanced_opts_selector\\\": \\\"show\\\", \\\"param_type\\\": {\\\"__current_case__\\\": 1, \\\"param_type_selector\\\": \\\"locarna\\\"}}\", \"merge_cluster_ol\": \"\\\"0.66\\\"\", \"iteration_num\": \"{\\\"__current_case__\\\": 1, \\\"iteration_num_selector\\\": \\\"false\\\"}\", \"cm_min_bitscore\": \"\\\"20\\\"\", \"cut_type\": \"\\\"false\\\"\", \"results_top_num\": \"\\\"5\\\"\", \"merge_overlap\": \"\\\"0.51\\\"\", \"cm_bitscore_sig\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"FASTA\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cmsearch_results\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cdhit\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"partition_type\": \"\\\"true\\\"\"}", "id": 11, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "f93c868203cc", "name": "graphclust_postprocessing", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "9a6f4913-35c4-4c8f-b297-fde0c5aeb3c6", "errors": null, "name": "cluster_collection_report", "post_job_actions": {"HideDatasetActiontableForEval": {"output_name": "tableForEval", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionpartitions": {"output_name": "partitions", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActioncombined_cm_out": {"output_name": "combined_cm_out", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_stats": {"output_name": "final_stats", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionevaluation": {"output_name": "evaluation", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_used_cmsearch": {"output_name": "final_used_cmsearch", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_soft": {"output_name": "final_soft", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [{"name": "cdhit", "description": "runtime parameter for tool cluster_collection_report"}], "position": {"top": 280.93750762939453, "left": 3270.011962890625}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5", "type": "tool"}, "12": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3.1", "tool_version": "9.2.3.1", "outputs": [{"type": "txt", "name": "fast_cluster"}, {"type": "txt", "name": "fast_cluster_sim"}, {"type": "txt", "name": "black_list"}, {"type": "txt", "name": "fast_cluster_m"}, {"type": "txt", "name": "fast_cluster_sim_m"}, {"type": "txt", "name": "black_list_m"}], "workflow_outputs": [{"output_name": "fast_cluster", "uuid": "c93a4fde-ed99-4d6a-91c2-1129a7a46682", "label": null}], "input_connections": {"iteration_num|blacklist": {"output_name": "black_list", "id": 5}, "iteration_num|fast_cluster_last_round": {"output_name": "fast_cluster", "id": 5}, "iteration_num|final_partition_soft": {"output_name": "final_soft", "id": 11}, "data_fasta": {"output_name": "data.fasta", "id": 1}, "data_names": {"output_name": "data.names", "id": 1}, "data_svector": {"output_name": "data_svector", "id": 4}}, "tool_state": "{\"knn\": \"\\\"10\\\"\", \"max_dist_relations\": \"\\\"3\\\"\", \"nhf\": \"\\\"500\\\"\", \"noCache\": \"\\\"true\\\"\", \"__page__\": null, \"usn\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"oc\": \"\\\"true\\\"\", \"iteration_num\": \"{\\\"CI\\\": \\\"2\\\", \\\"GLOBAL_hit_blacklist_overlap\\\": \\\"0.2\\\", \\\"__current_case__\\\": 0, \\\"blacklist\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fast_cluster_last_round\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"final_partition_soft\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"iteration_num_selector\\\": \\\"true\\\"}\", \"ensf\": \"\\\"5\\\"\", \"data_fasta\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"max_rad\": \"\\\"3\\\"\", \"data_svector\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"nspdk_nhf_max\": \"\\\"1000\\\"\", \"nspdk_nhf_step\": \"\\\"25\\\"\", \"GLOBAL_num_clusters\": \"\\\"100\\\"\", \"data_names\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", "id": 12, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "1b142e88d068", "name": "graphclust_nspdk", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "95e98cc4-d745-441d-a82f-5a5c6509bdde", "errors": null, "name": "NSPDK_candidateClusters", "post_job_actions": {"HideDatasetActionfast_cluster_sim_m": {"output_name": "fast_cluster_sim_m", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfast_cluster_m": {"output_name": "fast_cluster_m", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionblack_list": {"output_name": "black_list", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfast_cluster_sim": {"output_name": "fast_cluster_sim", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionblack_list_m": {"output_name": "black_list_m", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 200.00000381469727, "left": 3479.014404296875}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3.1", "type": "tool"}, "13": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4", "tool_version": "0.4", "outputs": [{"type": "input", "name": "centers"}, {"type": "input", "name": "trees"}, {"type": "input", "name": "cmFa"}, {"type": "input", "name": "model_tree_fa"}, {"type": "input", "name": "tree_matrix"}], "workflow_outputs": [], "input_connections": {"fasta_data": {"output_name": "data.fasta", "id": 1}, "fast_cluster_sim": {"output_name": "fast_cluster_sim_m", "id": 12}, "data_map": {"output_name": "data.map", "id": 1}, "fast_cluster": {"output_name": "fast_cluster_m", "id": 12}}, "tool_state": "{\"knn\": \"\\\"10\\\"\", \"__page__\": null, \"CI\": \"\\\"2\\\"\", \"fasta_data\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"fast_cluster_sim\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"data_map\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"fast_cluster\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", "id": 13, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "5c92a3f7b59c", "name": "graphclust_prepocessing_for_mlocarna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "b1ba27a3-a9b9-43e3-8552-f3d48f478cc4", "errors": null, "name": "pgma_graphclust", "post_job_actions": {"HideDatasetActioncmFa": {"output_name": "cmFa", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiontrees": {"output_name": "trees", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActioncenters": {"output_name": "centers", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiontree_matrix": {"output_name": "tree_matrix", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionmodel_tree_fa": {"output_name": "model_tree_fa", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 3821.9951171875}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4", "type": "tool"}, "14": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4", "tool_version": "0.4", "outputs": [{"type": "stockholm", "name": "model_tree_stk"}], "workflow_outputs": [], "input_connections": {"tree_file": {"output_name": "trees", "id": 13}, "data_map": {"output_name": "data.map", "id": 1}, "center_fa_file": {"output_name": "centers", "id": 13}, "tree_matrix": {"output_name": "tree_matrix", "id": 13}}, "tool_state": "{\"tau\": \"\\\"50\\\"\", \"max_diff_am\": \"\\\"50\\\"\", \"center_fa_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"free_endgaps\": \"\\\"0\\\"\", \"tree_matrix\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"p\": \"\\\"0.001\\\"\", \"allow_overlap\": \"\\\"false\\\"\", \"data_map\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"param_type\": \"{\\\"__current_case__\\\": 0, \\\"alifold_consensus_dp\\\": \\\"true\\\", \\\"indel\\\": \\\"-200\\\", \\\"indel_opening\\\": \\\"-400\\\", \\\"max_diff\\\": \\\"100\\\", \\\"max_diff_am\\\": \\\"50\\\", \\\"p\\\": \\\"0.001\\\", \\\"param_type_selector\\\": \\\"gclust\\\", \\\"plfold_minlen\\\": \\\"210\\\", \\\"plfold_span\\\": \\\"150\\\", \\\"plfold_winsize\\\": \\\"300\\\", \\\"struct_weight\\\": \\\"180\\\", \\\"tau\\\": \\\"50\\\"}\", \"max_diff\": \"\\\"100\\\"\", \"tree_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"plfold_minlen\": \"\\\"210\\\"\"}", "id": 14, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "c45eef4517d9", "name": "graphclust_mlocarna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "e0821ae8-5367-4351-91fc-5f268e741481", "errors": null, "name": "locarna_graphclust", "post_job_actions": {"HideDatasetActionmodel_tree_stk": {"output_name": "model_tree_stk", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 4053.016845703125}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4", "type": "tool"}, "15": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4", "tool_version": "0.4", "outputs": [{"type": "stockholm", "name": "model_cmfinder_stk"}], "workflow_outputs": [{"output_name": "model_cmfinder_stk", "uuid": "4a0a6667-8ff0-4a16-9b54-9357f9311dca", "label": null}], "input_connections": {"model_tree_stk": {"output_name": "model_tree_stk", "id": 14}, "cmfinder_fa": {"output_name": "cmFa", "id": 13}}, "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cmfinder_fa\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"model_tree_stk\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"gap_threshold_opts\": \"{\\\"__current_case__\\\": 0, \\\"gap\\\": \\\"1.0\\\", \\\"gap_threshold_opts_selector\\\": \\\"--g\\\"}\"}", "id": 15, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "5a1dcc77b0ce", "name": "graphclust_cmfinder", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "63318a43-c200-4e40-a041-af1c5d88a76d", "errors": null, "name": "cmfinder", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 4315}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4", "type": "tool"}, "16": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0", "tool_version": "1.1.2.0", "outputs": [{"type": "text", "name": "summary_outfile"}, {"type": "cm", "name": "cmfile_outfile"}, {"type": "stockholm", "name": "refined_multiple_alignment_output"}, {"type": "txt", "name": "hfile"}, {"type": "txt", "name": "sfile"}, {"type": "txt", "name": "qqfile"}, {"type": "txt", "name": "ffile"}, {"type": "txt", "name": "xfile"}], "workflow_outputs": [{"output_name": "cmfile_outfile", "uuid": "8b09ae66-ffa7-4321-8d36-dc489a4bc780", "label": null}], "input_connections": {"alignment_infile": {"output_name": "model_cmfinder_stk", "id": 15}}, "tool_state": "{\"__page__\": null, \"controlling_filter_p7_hmm\": \"{\\\"EgfN\\\": \\\"200\\\", \\\"ElfN\\\": \\\"200\\\", \\\"EmN\\\": \\\"200\\\", \\\"EvN\\\": \\\"200\\\", \\\"p7ere\\\": \\\"0.38\\\", \\\"p7ml\\\": \\\"false\\\"}\", \"noss\": \"\\\"false\\\"\", \"is_summery_output\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"effective_opts\": \"{\\\"__current_case__\\\": 0, \\\"effective_opts_selector\\\": \\\"--enone\\\"}\", \"alignment_infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"refining_opts\": \"{\\\"__current_case__\\\": 0, \\\"refining_opts_selector\\\": \\\"\\\"}\", \"Calibrate\": \"{\\\"L\\\": \\\"0.5\\\", \\\"__current_case__\\\": 1, \\\"add_opts\\\": {\\\"beta\\\": \\\"1e-15\\\", \\\"gc\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"nonbanded\\\": \\\"false\\\", \\\"nonull3\\\": \\\"false\\\", \\\"random\\\": \\\"false\\\", \\\"seed\\\": \\\"181\\\"}, \\\"cont_exp_tails_fits\\\": {\\\"__current_case__\\\": 0, \\\"gtailn\\\": \\\"250\\\", \\\"ltailn\\\": \\\"750\\\", \\\"selector\\\": \\\"top_n\\\"}, \\\"output_options_cond\\\": {\\\"__current_case__\\\": 1, \\\"selector\\\": \\\"none\\\"}, \\\"selector\\\": \\\"true\\\"}\", \"model_construction_opts\": \"{\\\"__current_case__\\\": 0, \\\"model_construction_opts_selector\\\": \\\"--fast\\\", \\\"symfrac\\\": \\\"0.5\\\"}\", \"relative_weights_opts\": \"{\\\"__current_case__\\\": 0, \\\"relative_weights_opts_selector\\\": \\\"--wpb\\\"}\"}", "id": 16, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "477d829d3250", "name": "infernal", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "c4e3e0b3-b57b-46b3-bd10-95bc253ae545", "errors": null, "name": "cmbuild", "post_job_actions": {"HideDatasetActionsummary_outfile": {"output_name": "summary_outfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionrefined_multiple_alignment_output": {"output_name": "refined_multiple_alignment_output", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionffile": {"output_name": "ffile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionqqfile": {"output_name": "qqfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionxfile": {"output_name": "xfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionsfile": {"output_name": "sfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionhfile": {"output_name": "hfile", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 4603.0047607421875}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0", "type": "tool"}, "17": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0", "tool_version": "1.1.2.0", "outputs": [{"type": "tabular", "name": "outfile"}, {"type": "tabular", "name": "multiple_alignment_output"}], "workflow_outputs": [{"output_name": "outfile", "uuid": "25fcd304-c7b1-4d83-b50d-b5c9f9273a64", "label": null}], "input_connections": {"cm_opts|cmfile": {"output_name": "cmfile_outfile", "id": 16}, "seqdb": {"output_name": "data.fasta.scan", "id": 1}}, "tool_state": "{\"anytrunc\": \"\\\"false\\\"\", \"verbose\": \"\\\"false\\\"\", \"notrunc\": \"\\\"false\\\"\", \"smxsize\": \"\\\"128.0\\\"\", \"cm_opts\": \"{\\\"__current_case__\\\": 1, \\\"cm_opts_selector\\\": \\\"histdb\\\", \\\"cmfile\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"__page__\": null, \"bottomonly\": \"\\\"false\\\"\", \"seqdb\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"inclusion_thresholds_opts\": \"{\\\"__current_case__\\\": 0, \\\"inclusion_thresholds_selector\\\": \\\"\\\"}\", \"__rerun_remap_job_id__\": null, \"mxsize\": \"\\\"128.0\\\"\", \"A\": \"\\\"false\\\"\", \"acyk\": \"\\\"false\\\"\", \"acceleration_huristics\": \"{\\\"__current_case__\\\": 1, \\\"acceleration_huristics_selector\\\": \\\"--nohmm\\\"}\", \"reporting_thresholds_opts\": \"{\\\"__current_case__\\\": 0, \\\"reporting_thresholds_selector\\\": \\\"\\\"}\", \"cyk\": \"\\\"false\\\"\", \"Z\": \"\\\"\\\"\", \"model_thresholds\": \"{\\\"cut_ga\\\": \\\"false\\\", \\\"cut_nc\\\": \\\"false\\\", \\\"cut_tc\\\": \\\"false\\\"}\", \"g\": \"\\\"true\\\"\", \"nonull3\": \"\\\"false\\\"\", \"toponly\": \"\\\"true\\\"\", \"noali\": \"\\\"false\\\"\"}", "id": 17, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "477d829d3250", "name": "infernal", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "c4fd0658-01ee-4f35-b6bb-72a48e2ac2da", "errors": null, "name": "cmsearch", "post_job_actions": {"HideDatasetActionmultiple_alignment_output": {"output_name": "multiple_alignment_output", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 4930.99755859375}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0", "type": "tool"}, "18": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5", "tool_version": "0.5", "outputs": [{"type": "input", "name": "clusters"}, {"type": "input", "name": "allFasta"}, {"type": "input", "name": "partitions"}, {"type": "input", "name": "topSecondaryStruct"}, {"type": "input", "name": "topDot"}, {"type": "input", "name": "rscapePlot"}, {"type": "txt", "name": "final_stats"}, {"type": "tabular", "name": "tableForEval"}, {"type": "txt", "name": "final_soft"}, {"type": "txt", "name": "final_used_cmsearch"}, {"type": "txt", "name": "evaluation"}, {"type": "txt", "name": "combined_cm_out"}, {"type": "zip", "name": "RESULTS_zip"}], "workflow_outputs": [{"output_name": "topSecondaryStruct", "uuid": "0023b038-0de1-4eb7-a188-99d65a38a98c", "label": null}, {"output_name": "topDot", "uuid": "2841a0e7-431c-4439-9a84-f384179415db", "label": null}, {"output_name": "evaluation", "uuid": "4517a97b-98c5-49a4-b6ea-3d4f2b4ac66e", "label": null}, {"output_name": "RESULTS_zip", "uuid": "1a16392e-ef7f-49f2-84e9-0d2f068e43f0", "label": null}, {"output_name": "rscapePlot", "uuid": "785046a0-4168-454c-b199-4f8efbc85d4c", "label": null}], "input_connections": {"model_tree_files": {"output_name": "model_tree_fa", "id": 13}, "iteration_num|final_partition_used_cmsearch": {"output_name": "final_used_cmsearch", "id": 11}, "iteration_num|final_partition_soft": {"output_name": "final_soft", "id": 11}, "cmsearch_results": {"output_name": "outfile", "id": 17}, "iteration_num|combined_cm": {"output_name": "combined_cm_out", "id": 11}, "FASTA": {"output_name": "FASTA", "id": 1}}, "tool_state": "{\"__page__\": 0, \"model_tree_files\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cm_max_eval\": \"\\\"0.001\\\"\", \"min_cluster_size\": \"\\\"3\\\"\", \"advanced_opts\": \"{\\\"__current_case__\\\": 1, \\\"advanced_opts_selector\\\": \\\"show\\\", \\\"param_type\\\": {\\\"__current_case__\\\": 1, \\\"param_type_selector\\\": \\\"locarna\\\"}}\", \"merge_cluster_ol\": \"\\\"0.66\\\"\", \"iteration_num\": \"{\\\"CI\\\": \\\"2\\\", \\\"__current_case__\\\": 0, \\\"combined_cm\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"final_partition_soft\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"final_partition_used_cmsearch\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"iteration_num_selector\\\": \\\"true\\\"}\", \"cm_min_bitscore\": \"\\\"20\\\"\", \"cut_type\": \"\\\"false\\\"\", \"results_top_num\": \"\\\"5\\\"\", \"merge_overlap\": \"\\\"0.51\\\"\", \"cm_bitscore_sig\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"FASTA\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cmsearch_results\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cdhit\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"partition_type\": \"\\\"true\\\"\"}", "id": 18, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "f93c868203cc", "name": "graphclust_postprocessing", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "eb43d877-9b48-423d-af1f-62be6b0bd7b4", "errors": null, "name": "cluster_collection_report", "post_job_actions": {"HideDatasetActiontableForEval": {"output_name": "tableForEval", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActioncombined_cm_out": {"output_name": "combined_cm_out", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionpartitions": {"output_name": "partitions", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionallFasta": {"output_name": "allFasta", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionclusters": {"output_name": "clusters", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_stats": {"output_name": "final_stats", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_used_cmsearch": {"output_name": "final_used_cmsearch", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_soft": {"output_name": "final_soft", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [{"name": "cdhit", "description": "runtime parameter for tool cluster_collection_report"}], "position": {"top": 280.93750762939453, "left": 5236.983154296875}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5", "type": "tool"}, "19": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3.1", "tool_version": "9.2.3.1", "outputs": [{"type": "txt", "name": "fast_cluster"}, {"type": "txt", "name": "fast_cluster_sim"}, {"type": "txt", "name": "black_list"}, {"type": "txt", "name": "fast_cluster_m"}, {"type": "txt", "name": "fast_cluster_sim_m"}, {"type": "txt", "name": "black_list_m"}], "workflow_outputs": [{"output_name": "black_list_m", "uuid": "81d64fe7-70f9-43d5-aeb2-50a7a113db9a", "label": null}, {"output_name": "fast_cluster", "uuid": "aebbf185-157e-4613-8956-166b839a9624", "label": null}, {"output_name": "fast_cluster_m", "uuid": "a9800a53-6368-44d7-98c4-2c55755de63e", "label": null}], "input_connections": {"iteration_num|blacklist": {"output_name": "black_list_m", "id": 12}, "iteration_num|fast_cluster_last_round": {"output_name": "fast_cluster_m", "id": 12}, "iteration_num|final_partition_soft": {"output_name": "final_soft", "id": 18}, "data_fasta": {"output_name": "data.fasta", "id": 1}, "data_names": {"output_name": "data.names", "id": 1}, "data_svector": {"output_name": "data_svector", "id": 4}}, "tool_state": "{\"knn\": \"\\\"10\\\"\", \"max_dist_relations\": \"\\\"3\\\"\", \"nhf\": \"\\\"500\\\"\", \"noCache\": \"\\\"true\\\"\", \"__page__\": null, \"usn\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"oc\": \"\\\"true\\\"\", \"iteration_num\": \"{\\\"CI\\\": \\\"3\\\", \\\"GLOBAL_hit_blacklist_overlap\\\": \\\"0.2\\\", \\\"__current_case__\\\": 0, \\\"blacklist\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fast_cluster_last_round\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"final_partition_soft\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"iteration_num_selector\\\": \\\"true\\\"}\", \"ensf\": \"\\\"5\\\"\", \"data_fasta\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"max_rad\": \"\\\"3\\\"\", \"data_svector\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"nspdk_nhf_max\": \"\\\"1000\\\"\", \"nspdk_nhf_step\": \"\\\"25\\\"\", \"GLOBAL_num_clusters\": \"\\\"100\\\"\", \"data_names\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", "id": 19, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "1b142e88d068", "name": "graphclust_nspdk", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "0570418e-eff8-4854-a271-5e50cd6f6df5", "errors": null, "name": "NSPDK_candidateClusters", "post_job_actions": {"HideDatasetActionfast_cluster_sim_m": {"output_name": "fast_cluster_sim_m", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionblack_list": {"output_name": "black_list", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfast_cluster_sim": {"output_name": "fast_cluster_sim", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 292.93270111083984, "left": 5477.99267578125}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3.1", "type": "tool"}, "20": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4", "tool_version": "0.4", "outputs": [{"type": "input", "name": "centers"}, {"type": "input", "name": "trees"}, {"type": "input", "name": "cmFa"}, {"type": "input", "name": "model_tree_fa"}, {"type": "input", "name": "tree_matrix"}], "workflow_outputs": [], "input_connections": {"fasta_data": {"output_name": "data.fasta", "id": 1}, "fast_cluster_sim": {"output_name": "fast_cluster_sim_m", "id": 19}, "data_map": {"output_name": "data.map", "id": 1}, "fast_cluster": {"output_name": "fast_cluster_m", "id": 19}}, "tool_state": "{\"knn\": \"\\\"10\\\"\", \"__page__\": null, \"CI\": \"\\\"3\\\"\", \"fasta_data\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"fast_cluster_sim\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"data_map\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"fast_cluster\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", "id": 20, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "5c92a3f7b59c", "name": "graphclust_prepocessing_for_mlocarna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "52413bb2-08cf-42e0-b6c4-9c3d92b1dae3", "errors": null, "name": "pgma_graphclust", "post_job_actions": {"HideDatasetActioncmFa": {"output_name": "cmFa", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiontrees": {"output_name": "trees", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActioncenters": {"output_name": "centers", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionmodel_tree_fa": {"output_name": "model_tree_fa", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActiontree_matrix": {"output_name": "tree_matrix", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 5790.99755859375}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4", "type": "tool"}, "21": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4", "tool_version": "0.4", "outputs": [{"type": "stockholm", "name": "model_tree_stk"}], "workflow_outputs": [{"output_name": "model_tree_stk", "uuid": "4c0e6649-ef9f-4955-8a95-af464d21b0c6", "label": null}], "input_connections": {"tree_file": {"output_name": "trees", "id": 20}, "data_map": {"output_name": "data.map", "id": 1}, "center_fa_file": {"output_name": "centers", "id": 20}, "tree_matrix": {"output_name": "tree_matrix", "id": 20}}, "tool_state": "{\"__page__\": null, \"center_fa_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"free_endgaps\": \"\\\"0\\\"\", \"tree_matrix\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"allow_overlap\": \"\\\"false\\\"\", \"data_map\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"param_type\": \"{\\\"__current_case__\\\": 0, \\\"alifold_consensus_dp\\\": \\\"true\\\", \\\"indel\\\": \\\"-200\\\", \\\"indel_opening\\\": \\\"-400\\\", \\\"max_diff\\\": \\\"100\\\", \\\"max_diff_am\\\": \\\"50\\\", \\\"p\\\": \\\"0.001\\\", \\\"param_type_selector\\\": \\\"gclust\\\", \\\"plfold_minlen\\\": \\\"210\\\", \\\"plfold_span\\\": \\\"150\\\", \\\"plfold_winsize\\\": \\\"300\\\", \\\"struct_weight\\\": \\\"180\\\", \\\"tau\\\": \\\"50\\\"}\", \"tree_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", "id": 21, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "c45eef4517d9", "name": "graphclust_mlocarna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "c2109e04-a7d6-4641-86d3-16858cb17b8a", "errors": null, "name": "locarna_graphclust", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 6021.9591064453125}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4", "type": "tool"}, "22": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4", "tool_version": "0.4", "outputs": [{"type": "stockholm", "name": "model_cmfinder_stk"}], "workflow_outputs": [{"output_name": "model_cmfinder_stk", "uuid": "40b61018-3337-4f4a-80b0-1857d57c7973", "label": null}], "input_connections": {"model_tree_stk": {"output_name": "model_tree_stk", "id": 21}, "cmfinder_fa": {"output_name": "cmFa", "id": 20}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"cmfinder_fa\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"model_tree_stk\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"gap_threshold_opts\": \"{\\\"__current_case__\\\": 0, \\\"gap\\\": \\\"1.0\\\", \\\"gap_threshold_opts_selector\\\": \\\"--g\\\"}\"}", "id": 22, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "5a1dcc77b0ce", "name": "graphclust_cmfinder", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "bd22f091-92a0-4b25-bed0-7da2bd517c1b", "errors": null, "name": "cmfinder", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 6283.9903564453125}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4", "type": "tool"}, "23": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0", "tool_version": "1.1.2.0", "outputs": [{"type": "text", "name": "summary_outfile"}, {"type": "cm", "name": "cmfile_outfile"}, {"type": "stockholm", "name": "refined_multiple_alignment_output"}, {"type": "txt", "name": "hfile"}, {"type": "txt", "name": "sfile"}, {"type": "txt", "name": "qqfile"}, {"type": "txt", "name": "ffile"}, {"type": "txt", "name": "xfile"}], "workflow_outputs": [{"output_name": "cmfile_outfile", "uuid": "2dccd67e-a217-4a85-9b35-17f6fa26b03d", "label": null}], "input_connections": {"alignment_infile": {"output_name": "model_cmfinder_stk", "id": 22}}, "tool_state": "{\"__page__\": null, \"controlling_filter_p7_hmm\": \"{\\\"EgfN\\\": \\\"200\\\", \\\"ElfN\\\": \\\"200\\\", \\\"EmN\\\": \\\"200\\\", \\\"EvN\\\": \\\"200\\\", \\\"p7ere\\\": \\\"0.38\\\", \\\"p7ml\\\": \\\"false\\\"}\", \"noss\": \"\\\"false\\\"\", \"is_summery_output\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"effective_opts\": \"{\\\"__current_case__\\\": 0, \\\"effective_opts_selector\\\": \\\"--enone\\\"}\", \"alignment_infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"refining_opts\": \"{\\\"__current_case__\\\": 0, \\\"refining_opts_selector\\\": \\\"\\\"}\", \"Calibrate\": \"{\\\"L\\\": \\\"0.5\\\", \\\"__current_case__\\\": 1, \\\"add_opts\\\": {\\\"beta\\\": \\\"1e-15\\\", \\\"gc\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"nonbanded\\\": \\\"false\\\", \\\"nonull3\\\": \\\"false\\\", \\\"random\\\": \\\"false\\\", \\\"seed\\\": \\\"181\\\"}, \\\"cont_exp_tails_fits\\\": {\\\"__current_case__\\\": 0, \\\"gtailn\\\": \\\"250\\\", \\\"ltailn\\\": \\\"750\\\", \\\"selector\\\": \\\"top_n\\\"}, \\\"output_options_cond\\\": {\\\"__current_case__\\\": 1, \\\"selector\\\": \\\"none\\\"}, \\\"selector\\\": \\\"true\\\"}\", \"model_construction_opts\": \"{\\\"__current_case__\\\": 0, \\\"model_construction_opts_selector\\\": \\\"--fast\\\", \\\"symfrac\\\": \\\"0.5\\\"}\", \"relative_weights_opts\": \"{\\\"__current_case__\\\": 0, \\\"relative_weights_opts_selector\\\": \\\"--wpb\\\"}\"}", "id": 23, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "477d829d3250", "name": "infernal", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "beebaa3c-e1ef-4eef-b6f4-34f808aa42bb", "errors": null, "name": "cmbuild", "post_job_actions": {"HideDatasetActionsummary_outfile": {"output_name": "summary_outfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionrefined_multiple_alignment_output": {"output_name": "refined_multiple_alignment_output", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionffile": {"output_name": "ffile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionqqfile": {"output_name": "qqfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionxfile": {"output_name": "xfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionsfile": {"output_name": "sfile", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionhfile": {"output_name": "hfile", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 6572.007173538208}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0", "type": "tool"}, "24": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0", "tool_version": "1.1.2.0", "outputs": [{"type": "tabular", "name": "outfile"}, {"type": "tabular", "name": "multiple_alignment_output"}], "workflow_outputs": [{"output_name": "multiple_alignment_output", "uuid": "9314cfc4-4375-4aef-8685-1e97cd5aafb2", "label": null}], "input_connections": {"cm_opts|cmfile": {"output_name": "cmfile_outfile", "id": 23}, "seqdb": {"output_name": "data.fasta.scan", "id": 1}}, "tool_state": "{\"anytrunc\": \"\\\"false\\\"\", \"verbose\": \"\\\"false\\\"\", \"notrunc\": \"\\\"false\\\"\", \"smxsize\": \"\\\"128.0\\\"\", \"cm_opts\": \"{\\\"__current_case__\\\": 1, \\\"cm_opts_selector\\\": \\\"histdb\\\", \\\"cmfile\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"__page__\": null, \"bottomonly\": \"\\\"false\\\"\", \"seqdb\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"inclusion_thresholds_opts\": \"{\\\"__current_case__\\\": 0, \\\"inclusion_thresholds_selector\\\": \\\"\\\"}\", \"__rerun_remap_job_id__\": null, \"mxsize\": \"\\\"128.0\\\"\", \"A\": \"\\\"false\\\"\", \"acyk\": \"\\\"false\\\"\", \"acceleration_huristics\": \"{\\\"__current_case__\\\": 1, \\\"acceleration_huristics_selector\\\": \\\"--nohmm\\\"}\", \"reporting_thresholds_opts\": \"{\\\"__current_case__\\\": 0, \\\"reporting_thresholds_selector\\\": \\\"\\\"}\", \"cyk\": \"\\\"false\\\"\", \"Z\": \"\\\"\\\"\", \"model_thresholds\": \"{\\\"cut_ga\\\": \\\"false\\\", \\\"cut_nc\\\": \\\"false\\\", \\\"cut_tc\\\": \\\"false\\\"}\", \"g\": \"\\\"true\\\"\", \"nonull3\": \"\\\"false\\\"\", \"toponly\": \"\\\"true\\\"\", \"noali\": \"\\\"false\\\"\"}", "id": 24, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "477d829d3250", "name": "infernal", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "b2cb6448-e66a-4dcc-ba8d-b0fc1053f78e", "errors": null, "name": "cmsearch", "post_job_actions": {"HideDatasetActionoutfile": {"output_name": "outfile", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 280.93750762939453, "left": 6900.011993408203}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0", "type": "tool"}, "25": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5", "tool_version": "0.5", "outputs": [{"type": "input", "name": "clusters"}, {"type": "input", "name": "allFasta"}, {"type": "input", "name": "partitions"}, {"type": "input", "name": "topSecondaryStruct"}, {"type": "input", "name": "topDot"}, {"type": "input", "name": "rscapePlot"}, {"type": "txt", "name": "final_stats"}, {"type": "tabular", "name": "tableForEval"}, {"type": "txt", "name": "final_soft"}, {"type": "txt", "name": "final_used_cmsearch"}, {"type": "txt", "name": "evaluation"}, {"type": "txt", "name": "combined_cm_out"}, {"type": "zip", "name": "RESULTS_zip"}], "workflow_outputs": [{"output_name": "topDot", "uuid": "150200ac-353b-4a1d-91c3-16ef341c7ed6", "label": null}, {"output_name": "allFasta", "uuid": "26ddd976-7f88-468f-b9d6-592593a4ed48", "label": null}, {"output_name": "rscapePlot", "uuid": "b98bbc36-39f3-42b0-94c9-a2abe28dff88", "label": null}, {"output_name": "topSecondaryStruct", "uuid": "7b94d415-a65f-4818-a212-704262cd0560", "label": null}, {"output_name": "evaluation", "uuid": "d46a702a-21ab-4de4-a303-59512b12acde", "label": null}, {"output_name": "RESULTS_zip", "uuid": "d4683b17-b93b-4e6f-bbb5-0e0bcd1ad597", "label": null}], "input_connections": {"model_tree_files": {"output_name": "model_tree_fa", "id": 20}, "iteration_num|final_partition_used_cmsearch": {"output_name": "final_used_cmsearch", "id": 18}, "iteration_num|final_partition_soft": {"output_name": "final_soft", "id": 18}, "cmsearch_results": {"output_name": "outfile", "id": 24}, "iteration_num|combined_cm": {"output_name": "combined_cm_out", "id": 18}, "FASTA": {"output_name": "FASTA", "id": 1}}, "tool_state": "{\"__page__\": null, \"model_tree_files\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cm_max_eval\": \"\\\"0.001\\\"\", \"min_cluster_size\": \"\\\"3\\\"\", \"advanced_opts\": \"{\\\"__current_case__\\\": 0, \\\"advanced_opts_selector\\\": \\\"hide\\\"}\", \"merge_cluster_ol\": \"\\\"0.66\\\"\", \"iteration_num\": \"{\\\"CI\\\": \\\"3\\\", \\\"__current_case__\\\": 0, \\\"combined_cm\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"final_partition_soft\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"final_partition_used_cmsearch\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"iteration_num_selector\\\": \\\"true\\\"}\", \"cm_min_bitscore\": \"\\\"20\\\"\", \"cut_type\": \"\\\"false\\\"\", \"results_top_num\": \"\\\"5\\\"\", \"merge_overlap\": \"\\\"0.51\\\"\", \"cm_bitscore_sig\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"FASTA\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cmsearch_results\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"cdhit\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"partition_type\": \"\\\"true\\\"\"}", "id": 25, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "f93c868203cc", "name": "graphclust_postprocessing", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "8b8abcdd-c96e-4cae-9fb6-a2176a4d65e5", "errors": null, "name": "cluster_collection_report", "post_job_actions": {"HideDatasetActiontableForEval": {"output_name": "tableForEval", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionpartitions": {"output_name": "partitions", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActioncombined_cm_out": {"output_name": "combined_cm_out", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionclusters": {"output_name": "clusters", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_stats": {"output_name": "final_stats", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_used_cmsearch": {"output_name": "final_used_cmsearch", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionfinal_soft": {"output_name": "final_soft", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [{"name": "cdhit", "description": "runtime parameter for tool cluster_collection_report"}], "position": {"top": 267.94471740722656, "left": 7213.016784667969}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}