{"uuid": "c9096a6f-5efb-4ca6-a366-3c9e6431609c", "tags": ["covid-19"], "format-version": "0.1", "name": "MC_COVID19like_Assembly_Reads", "version": 12, "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "f5978cd3-ac2f-4ccc-a665-a8431a9a73d9", "label": null}], "input_connections": {}, "tool_state": "{\"optional\": false}", "id": 0, "uuid": "b4ebcec8-234f-4e2e-9b0a-19052bc27a68", "errors": null, "name": "Input dataset", "label": "Forward reads", "inputs": [], "position": {"top": 699.2666625976562, "left": 200}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "a2bd6dd8-98a0-4a7a-b516-b8fbbf76a117", "label": null}], "input_connections": {}, "tool_state": "{}", "id": 1, "uuid": "4ecad17b-0845-40aa-a74b-41d4bcee055f", "errors": null, "name": "Input dataset", "label": "Reverse read", "inputs": [], "position": {"top": 875.816650390625, "left": 185.03334045410156}, "annotation": "", "content_id": null, "type": "data_input"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "tool_version": "2.3.4.3+galaxy0", "outputs": [{"type": "fastqsanger", "name": "output_unaligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_r"}, {"type": "fastqsanger", "name": "output_unaligned_reads_r"}, {"type": "bam", "name": "output"}, {"type": "txt", "name": "mapping_stats"}], "workflow_outputs": [{"output_name": "output_unaligned_reads_l", "uuid": "b892d63d-2a40-445f-9d34-915a0eecfefa", "label": null}, {"output_name": "output_unaligned_reads_r", "uuid": "a164716a-f851-4b88-b3d9-c503031cf37e", "label": null}], "input_connections": {"library|input_2": {"output_name": "output", "id": 1}, "library|input_1": {"output_name": "output", "id": 0}}, "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 1, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"input_2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"--very-sensitive-local\\\"}\"}", "id": 2, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "749c918495f7", "name": "bowtie2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "23514da4-7b47-47fa-b516-ac5ee41460ed", "errors": null, "name": "Bowtie2", "post_job_actions": {"HideDatasetActionoutput_aligned_reads_r": {"output_name": "output_aligned_reads_r", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput_aligned_reads_l": {"output_name": "output_aligned_reads_l", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionmapping_stats": {"output_name": "mapping_stats", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput": {"output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": "Filter_human_reads", "inputs": [{"name": "library", "description": "runtime parameter for tool Bowtie2"}, {"name": "library", "description": "runtime parameter for tool Bowtie2"}], "position": {"top": 752.4666748046875, "left": 440.2333526611328}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "type": "tool"}, "3": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1", "tool_version": "0.19.5+galaxy1", "outputs": [{"type": "input", "name": "output_paired_coll"}, {"type": "input", "name": "out1"}, {"type": "input", "name": "out2"}, {"type": "html", "name": "report_html"}, {"type": "json", "name": "report_json"}], "workflow_outputs": [{"output_name": "out1", "uuid": "a90c157e-6e2d-43d9-836a-ad60a8f96bc2", "label": null}, {"output_name": "out2", "uuid": "d22973f1-1940-4f54-90ef-91c9cb15f375", "label": null}, {"output_name": "report_html", "uuid": "a5ff7773-6b19-4330-98ba-b529638be456", "label": null}], "input_connections": {"single_paired|in2": {"output_name": "output_unaligned_reads_r", "id": 2}, "single_paired|in1": {"output_name": "output_unaligned_reads_l", "id": 2}}, "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"true\\\", \\\"report_json\\\": \\\"false\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 1, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"in1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"in2\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"single_paired_selector\\\": \\\"paired\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"true\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"40\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"25\\\", \\\"enable_low_complexity_filter\\\": \\\"true\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"\\\", \\\"unqualified_percent_limit\\\": \\\"\\\"}}\", \"__rerun_remap_job_id__\": null}", "id": 3, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "1d8fe9bc4cb0", "name": "fastp", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "0264250a-be98-4d56-b0ab-11cf0a9f2ce6", "errors": null, "name": "fastp", "post_job_actions": {"HideDatasetActionreport_json": {"output_name": "report_json", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput_paired_coll": {"output_name": "output_paired_coll", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [], "position": {"top": 735.7999877929688, "left": 833.0333404541016}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1", "type": "tool"}, "4": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "tool_version": "2.3.4.3+galaxy0", "outputs": [{"type": "fastqsanger", "name": "output_unaligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_r"}, {"type": "fastqsanger", "name": "output_unaligned_reads_r"}, {"type": "bam", "name": "output"}, {"type": "txt", "name": "mapping_stats"}], "workflow_outputs": [{"output_name": "output", "uuid": "0df6d3b9-9ce3-493d-8bec-61c761284bdf", "label": null}, {"output_name": "output_aligned_reads_l", "uuid": "d2d8b752-22b2-4384-81bc-96a4d2147fe2", "label": null}, {"output_name": "output_aligned_reads_r", "uuid": "0f82e2e4-110d-4df6-a1ea-e9208f3d05d3", "label": null}, {"output_name": "mapping_stats", "uuid": "d4007a80-640b-4bf0-8aaa-d0664c6644ac", "label": null}], "input_connections": {"library|input_2": {"output_name": "out2", "id": 3}, "library|input_1": {"output_name": "out1", "id": 3}}, "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 1, \\\"aligned_file\\\": \\\"true\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"input_2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 1, \\\"own_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"source\\\": \\\"history\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"--very-sensitive-local\\\"}\"}", "id": 4, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "749c918495f7", "name": "bowtie2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5120a2de-14cb-4c03-a81b-a8519cf68239", "errors": null, "name": "Bowtie2", "post_job_actions": {"RenameDatasetActionoutput_aligned_reads_r": {"output_name": "output_aligned_reads_r", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "SARS-CoV-2_like_reads.R.fastq"}}, "HideDatasetActionoutput_unaligned_reads_r": {"output_name": "output_unaligned_reads_r", "action_type": "HideDatasetAction", "action_arguments": {}}, "RenameDatasetActionoutput_aligned_reads_l": {"output_name": "output_aligned_reads_l", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "SARS-CoV-2_like_reads.L.fastq"}}, "HideDatasetActionoutput_unaligned_reads_l": {"output_name": "output_unaligned_reads_l", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": "Any_SARS-CoV-2_reads", "inputs": [{"name": "library", "description": "runtime parameter for tool Bowtie2"}, {"name": "library", "description": "runtime parameter for tool Bowtie2"}, {"name": "reference_genome", "description": "runtime parameter for tool Bowtie2"}], "position": {"top": 729.2666625976562, "left": 1114.0333404541016}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "type": "tool"}, "5": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0", "tool_version": "0.4.6.0", "outputs": [{"type": "tabular", "name": "assembly_graph"}, {"type": "fasta", "name": "assembly"}], "workflow_outputs": [{"output_name": "assembly", "uuid": "e44c5d37-1a7c-4617-b871-8f94b07a981d", "label": null}], "input_connections": {"paired_unpaired|fastq_input2": {"output_name": "output_aligned_reads_r", "id": 4}, "paired_unpaired|fastq_input1": {"output_name": "output_aligned_reads_l", "id": 4}}, "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"1000\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}", "id": 5, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "23300b42ca18", "name": "unicycler", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "d89c0df2-28d4-491a-b427-3527540c95ad", "errors": null, "name": "Create assemblies with Unicycler", "post_job_actions": {"HideDatasetActionassembly_graph": {"output_name": "assembly_graph", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [{"name": "lr_align", "description": "runtime parameter for tool Create assemblies with Unicycler"}, {"name": "long", "description": "runtime parameter for tool Create assemblies with Unicycler"}, {"name": "rotation", "description": "runtime parameter for tool Create assemblies with Unicycler"}], "position": {"top": 580.2666625976562, "left": 1432.0333404541016}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0", "type": "tool"}, "6": {"tool_id": "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1", "tool_version": "3.12.0+galaxy1", "outputs": [{"type": "tabular", "name": "out_contig_stats"}, {"type": "tabular", "name": "out_scaffold_stats"}, {"type": "fasta", "name": "out_contigs"}, {"type": "fasta", "name": "out_scaffolds"}, {"type": "txt", "name": "out_log"}, {"type": "txt", "name": "contig_graph"}, {"type": "txt", "name": "scaffold_graph"}], "workflow_outputs": [{"output_name": "out_scaffolds", "uuid": "772888c5-a31d-4d12-9f6d-f8d09dedfdfd", "label": null}, {"output_name": "out_scaffold_stats", "uuid": "8b560fc7-be85-4298-8287-a57ee7638d40", "label": null}], "input_connections": {"libraries_0|files_0|file_type|rev_reads": {"output_name": "output_aligned_reads_r", "id": 4}, "libraries_0|files_0|file_type|fwd_reads": {"output_name": "output_aligned_reads_l", "id": 4}}, "tool_state": "{\"pacbio_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"libraries\": \"[{\\\"__index__\\\": 0, \\\"files\\\": [{\\\"__index__\\\": 0, \\\"file_type\\\": {\\\"__current_case__\\\": 0, \\\"fwd_reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"rev_reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"separate\\\"}}], \\\"lib_type\\\": \\\"paired_end\\\", \\\"orientation\\\": \\\"fr\\\"}]\", \"iontorrent\": \"\\\"false\\\"\", \"cov\": \"{\\\"__current_case__\\\": 0, \\\"state\\\": \\\"off\\\"}\", \"__page__\": null, \"nanopore_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"trusted_contigs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"untrusted_contigs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"kmer_choice\": \"{\\\"__current_case__\\\": 0, \\\"auto_kmer_choice\\\": \\\"false\\\", \\\"kmers\\\": \\\"21,33,55,77\\\"}\", \"scaffold_graph_out\": \"\\\"false\\\"\", \"onlyassembler\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"sanger_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sc\": \"\\\"false\\\"\", \"careful\": \"\\\"true\\\"\", \"contig_graph_out\": \"\\\"false\\\"\"}", "id": 6, "tool_shed_repository": {"owner": "nml", "changeset_revision": "b8c00ce5dfa0", "name": "spades", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "6e4d3a3b-9b1a-4468-8df3-5d352b62f4bb", "errors": null, "name": "SPAdes", "post_job_actions": {"HideDatasetActionout_contigs": {"output_name": "out_contigs", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionout_contig_stats": {"output_name": "out_contig_stats", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionscaffold_graph": {"output_name": "scaffold_graph", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActioncontig_graph": {"output_name": "contig_graph", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionout_log": {"output_name": "out_log", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": null, "inputs": [{"name": "pacbio_reads", "description": "runtime parameter for tool SPAdes"}, {"name": "nanopore_reads", "description": "runtime parameter for tool SPAdes"}, {"name": "trusted_contigs", "description": "runtime parameter for tool SPAdes"}, {"name": "untrusted_contigs", "description": "runtime parameter for tool SPAdes"}, {"name": "sanger_reads", "description": "runtime parameter for tool SPAdes"}], "position": {"top": 994.2666625976562, "left": 1441.0333404541016}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1", "type": "tool"}, "7": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "tool_version": "2.3.4.3+galaxy0", "outputs": [{"type": "fastqsanger", "name": "output_unaligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_r"}, {"type": "fastqsanger", "name": "output_unaligned_reads_r"}, {"type": "bam", "name": "output"}, {"type": "txt", "name": "mapping_stats"}], "workflow_outputs": [{"output_name": "output_aligned_reads_l", "uuid": "699800cc-8d03-4af4-b9a8-175308bbfd7f", "label": null}, {"output_name": "output_aligned_reads_r", "uuid": "8a6d3f38-fae9-4baa-84b8-584984d419ec", "label": null}, {"output_name": "mapping_stats", "uuid": "d211daae-f87e-43eb-b5f3-4eca4109cb6e", "label": null}], "input_connections": {"library|input_2": {"output_name": "output_aligned_reads_r", "id": 4}, "library|input_1": {"output_name": "output_aligned_reads_l", "id": 4}, "reference_genome|own_file": {"output_name": "assembly", "id": 5}}, "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 1, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"input_2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"paired_options\\\": {\\\"I\\\": \\\"0\\\", \\\"X\\\": \\\"500\\\", \\\"__current_case__\\\": 0, \\\"dovetail\\\": \\\"false\\\", \\\"fr_rf_ff\\\": \\\"--fr\\\", \\\"no_contain\\\": \\\"true\\\", \\\"no_discordant\\\": \\\"false\\\", \\\"no_mixed\\\": \\\"false\\\", \\\"no_overlap\\\": \\\"true\\\", \\\"paired_options_selector\\\": \\\"yes\\\"}, \\\"type\\\": \\\"paired\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 1, \\\"own_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"source\\\": \\\"history\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 1, \\\"alignment_options\\\": {\\\"L\\\": \\\"24\\\", \\\"N\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"align_mode\\\": {\\\"__current_case__\\\": 0, \\\"align_mode_selector\\\": \\\"end-to-end\\\", \\\"score_min_ete\\\": \\\"L,0,0\\\"}, \\\"alignment_options_selector\\\": \\\"yes\\\", \\\"dpad\\\": \\\"15\\\", \\\"gbar\\\": \\\"4\\\", \\\"i\\\": \\\"S,1,1.15\\\", \\\"ignore_quals\\\": \\\"false\\\", \\\"n_ceil\\\": \\\"L,0,0.15\\\", \\\"no_1mm_upfront\\\": \\\"false\\\", \\\"nofw\\\": \\\"false\\\", \\\"norc\\\": \\\"false\\\"}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"effort_options\\\": {\\\"__current_case__\\\": 1, \\\"effort_options_selector\\\": \\\"no\\\"}, \\\"input_options\\\": {\\\"__current_case__\\\": 1, \\\"input_options_selector\\\": \\\"no\\\"}, \\\"other_options\\\": {\\\"__current_case__\\\": 1, \\\"other_options_selector\\\": \\\"no\\\"}, \\\"reporting_options\\\": {\\\"__current_case__\\\": 0, \\\"reporting_options_selector\\\": \\\"no\\\"}, \\\"scoring_options\\\": {\\\"__current_case__\\\": 1, \\\"scoring_options_selector\\\": \\\"no\\\"}}\"}", "id": 7, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "749c918495f7", "name": "bowtie2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "442e3faf-4807-4eb9-9e58-c5e53ca13adb", "errors": null, "name": "Bowtie2", "post_job_actions": {"RenameDatasetActionoutput_aligned_reads_r": {"output_name": "output_aligned_reads_r", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "Unicycler_identical_R.fastq"}}, "HideDatasetActionoutput_unaligned_reads_r": {"output_name": "output_unaligned_reads_r", "action_type": "HideDatasetAction", "action_arguments": {}}, "RenameDatasetActionoutput_aligned_reads_l": {"output_name": "output_aligned_reads_l", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "Unicycler_identical_L.fastq"}}, "HideDatasetActionoutput_unaligned_reads_l": {"output_name": "output_unaligned_reads_l", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput": {"output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": "Keep_identical_reads_Unicycler", "inputs": [{"name": "library", "description": "runtime parameter for tool Bowtie2"}, {"name": "library", "description": "runtime parameter for tool Bowtie2"}, {"name": "reference_genome", "description": "runtime parameter for tool Bowtie2"}], "position": {"top": 300, "left": 1779.2667388916016}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "type": "tool"}, "8": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "tool_version": "2.3.4.3+galaxy0", "outputs": [{"type": "fastqsanger", "name": "output_unaligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_l"}, {"type": "fastqsanger", "name": "output_aligned_reads_r"}, {"type": "fastqsanger", "name": "output_unaligned_reads_r"}, {"type": "bam", "name": "output"}, {"type": "txt", "name": "mapping_stats"}], "workflow_outputs": [{"output_name": "output_aligned_reads_l", "uuid": "55e56d40-9b13-4796-838a-81c2a94dfb42", "label": null}, {"output_name": "output_aligned_reads_r", "uuid": "28050325-e0cd-4f80-a655-ef7fb76413b8", "label": null}, {"output_name": "mapping_stats", "uuid": "e19dddf3-f92a-404e-8713-3356a4de9b3f", "label": null}], "input_connections": {"library|input_2": {"output_name": "output_aligned_reads_r", "id": 4}, "library|input_1": {"output_name": "output_aligned_reads_l", "id": 4}, "reference_genome|own_file": {"output_name": "out_scaffolds", "id": 6}}, "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 1, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"input_2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"paired_options\\\": {\\\"I\\\": \\\"0\\\", \\\"X\\\": \\\"500\\\", \\\"__current_case__\\\": 0, \\\"dovetail\\\": \\\"false\\\", \\\"fr_rf_ff\\\": \\\"--fr\\\", \\\"no_contain\\\": \\\"true\\\", \\\"no_discordant\\\": \\\"false\\\", \\\"no_mixed\\\": \\\"false\\\", \\\"no_overlap\\\": \\\"true\\\", \\\"paired_options_selector\\\": \\\"yes\\\"}, \\\"type\\\": \\\"paired\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 1, \\\"own_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"source\\\": \\\"history\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 1, \\\"alignment_options\\\": {\\\"L\\\": \\\"24\\\", \\\"N\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"align_mode\\\": {\\\"__current_case__\\\": 0, \\\"align_mode_selector\\\": \\\"end-to-end\\\", \\\"score_min_ete\\\": \\\"L,0,0\\\"}, \\\"alignment_options_selector\\\": \\\"yes\\\", \\\"dpad\\\": \\\"15\\\", \\\"gbar\\\": \\\"4\\\", \\\"i\\\": \\\"S,1,1.15\\\", \\\"ignore_quals\\\": \\\"false\\\", \\\"n_ceil\\\": \\\"L,0,0.15\\\", \\\"no_1mm_upfront\\\": \\\"false\\\", \\\"nofw\\\": \\\"false\\\", \\\"norc\\\": \\\"false\\\"}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"effort_options\\\": {\\\"__current_case__\\\": 1, \\\"effort_options_selector\\\": \\\"no\\\"}, \\\"input_options\\\": {\\\"__current_case__\\\": 1, \\\"input_options_selector\\\": \\\"no\\\"}, \\\"other_options\\\": {\\\"__current_case__\\\": 1, \\\"other_options_selector\\\": \\\"no\\\"}, \\\"reporting_options\\\": {\\\"__current_case__\\\": 0, \\\"reporting_options_selector\\\": \\\"no\\\"}, \\\"scoring_options\\\": {\\\"__current_case__\\\": 1, \\\"scoring_options_selector\\\": \\\"no\\\"}}\"}", "id": 8, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "749c918495f7", "name": "bowtie2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "e042d4b5-078a-40ab-8f37-72a16b6512ca", "errors": null, "name": "Bowtie2", "post_job_actions": {"RenameDatasetActionoutput_aligned_reads_r": {"output_name": "output_aligned_reads_r", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "SPAdes_identical_R.fastq"}}, "HideDatasetActionoutput_unaligned_reads_r": {"output_name": "output_unaligned_reads_r", "action_type": "HideDatasetAction", "action_arguments": {}}, "RenameDatasetActionoutput_aligned_reads_l": {"output_name": "output_aligned_reads_l", "action_type": "RenameDatasetAction", "action_arguments": {"newname": "SPADes_identical_L.fastq"}}, "HideDatasetActionoutput_unaligned_reads_l": {"output_name": "output_unaligned_reads_l", "action_type": "HideDatasetAction", "action_arguments": {}}, "HideDatasetActionoutput": {"output_name": "output", "action_type": "HideDatasetAction", "action_arguments": {}}}, "label": "Keep_identical_reads_SPAdes", "inputs": [{"name": "library", "description": "runtime parameter for tool Bowtie2"}, {"name": "library", "description": "runtime parameter for tool Bowtie2"}, {"name": "reference_genome", "description": "runtime parameter for tool Bowtie2"}], "position": {"top": 985.4666748046875, "left": 1790.2332916259766}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}