{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "rnaseq discover", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Rmdup", 
                    "name": "bam_paired_end_type"
                }
            ], 
            "name": "Rmdup", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 163, 
                "top": 212.5
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "samtools_rmdup", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"bam_paired_end_type\": \"{\\\"force_se\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"bam_paired_end_type_selector\\\": \\\"PE\\\", \\\"__current_case__\\\": 0}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {
                "input": {
                    "id": 0, 
                    "output_name": "output1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Cufflinks", 
                    "name": "lib"
                }
            ], 
            "name": "Cufflinks", 
            "outputs": [
                {
                    "name": "genes_expression", 
                    "type": "tabular"
                }, 
                {
                    "name": "transcripts_expression", 
                    "type": "tabular"
                }, 
                {
                    "name": "assembled_isoforms", 
                    "type": "gtf"
                }, 
                {
                    "name": "total_map_mass", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 475, 
                "top": 206.5
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "cufflinks", 
            "tool_state": "{\"reference_annotation\": \"{\\\"use_ref\\\": \\\"Use reference annotation guide\\\", \\\"reference_annotation_guide_file\\\": null, \\\"__current_case__\\\": 2}\", \"min_isoform_fraction\": \"\\\"0.1\\\"\", \"lib\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"singlePaired\": \"{\\\"sPaired\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"pre_mrna_fraction\": \"\\\"0.15\\\"\", \"bias_correction\": \"{\\\"do_bias_correction\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"max_intron_len\": \"\\\"5000\\\"\", \"input\": \"null\", \"global_model\": \"null\", \"do_normalization\": \"\\\"No\\\"\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}