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input},\n ]\n},\n{ step_name: \"stacks_6\", tool_name: \"ustacks\", rule_name: \"ustacks\",\n params: [\n { input_name: read_dir, origin_command: process_radtags_SE, origin_name: read_dir, origin_step: stacks_7},\n ]\n},\n{ step_name: \"stacks\", tool_name: \"cstacks\", rule_name: \"cstacks\",\n params: [\n { input_name: ustacks_done, origin_command: ustacks, origin_name: ustacks_done, origin_step: stacks_6},\n { input_name: popmap, origin_command: raw_popmap, origin_name: popmap, origin_step: input},\n ]\n},\n{ step_name: \"stacks_2\", tool_name: \"sstacks\", rule_name: \"sstacks\",\n params: [\n { input_name: cstacks_done, origin_command: cstacks, origin_name: cstacks_done, origin_step: stacks},\n { input_name: popmap, origin_command: raw_popmap, origin_name: popmap, origin_step: input},\n ]\n},\n{ step_name: \"stacks_3\", tool_name: \"tsv2bam\", rule_name: \"tsv2bam_SE\",\n params: [\n { input_name: sstacks_done, origin_command: sstacks, origin_name: sstacks_done, origin_step: stacks_2},\n { input_name: popmap, origin_command: raw_popmap, origin_name: popmap, origin_step: input},\n ]\n},\n{ step_name: \"stacks_4\", tool_name: \"gstacks_denovo\", rule_name: \"gstacks_denovo\",\n params: [\n { input_name: tsv2bam_done, origin_command: tsv2bam_SE, origin_name: tsv2bam_done, origin_step: stacks_3},\n { input_name: popmap, origin_command: raw_popmap, origin_name: popmap, origin_step: input},\n ]\n},\n{ step_name: \"stacks_5\", tool_name: \"populations\", rule_name: \"populations\",\n params: [\n { input_name: catalog_calls, origin_command: gstacks_denovo, origin_name: catalog_calls, origin_step: stacks_4},\n { input_name: popmap, origin_command: raw_popmap, origin_name: popmap, origin_step: input},\n ]\n},\n],\nsteps: [\n { title: \"stacks_7\", name: \"stacks_7\", tools: [process_radtags], default: \"process_radtags\" },\n { title: \"stacks_6\", name: \"stacks_6\", tools: [ustacks], default: \"ustacks\" },\n { title: \"stacks\", name: \"stacks\", tools: [cstacks], default: \"cstacks\" },\n { title: \"stacks_2\", name: \"stacks_2\", tools: [sstacks], default: \"sstacks\" },\n { title: \"stacks_3\", name: \"stacks_3\", tools: [tsv2bam], default: \"tsv2bam\" },\n { title: \"stacks_4\", name: \"stacks_4\", tools: [gstacks_denovo], default: \"gstacks_denovo\" },\n { title: \"stacks_5\", name: \"stacks_5\", tools: [populations], default: \"populations\" },\n],\ninput: [\"raw_SE_read_dir\",\"raw_tsv\",\"raw_popmap\",],\nparams_equals: [\n { param_A: \"stacks_5__populations_popmap\", param_B: \"stacks__cstacks_popmap\"},\n { param_A: \"stacks_5__populations_popmap\", param_B: \"stacks_2__sstacks_popmap\"},\n { param_A: \"stacks_5__populations_popmap\", param_B: \"stacks_3__tsv2bam_SE_popmap\"},\n { param_A: \"stacks_5__populations_popmap\", param_B: \"stacks_4__gstacks_denovo_popmap\"},\n\n]\n}\n" } ]