{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Detrprok_current", 
    "steps": {
        "0": {
            "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
                    "name": "positions list of all genome known annotations"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 166, 
                "top": 364
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"positions list of all genome known annotations\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", 
                    "name": "read alignments on genome"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 215, 
                "top": 484
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"read alignments on genome\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {
                "inputFile": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "clean Gff", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 361, 
                "top": 327
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/cleanGff/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"type\": \"\\\"tRNA,rRNA,ncRNA,CDS\\\"\", \"inputFile\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "Technical step (format change).", 
            "id": 3, 
            "input_connections": {
                "input1": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "BAM-to-SAM", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "sam"
                }
            ], 
            "position": {
                "left": 418, 
                "top": 479
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutput1": {
                    "action_arguments": {
                        "newname": "Read alignments in SAM format"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "bam_to_sam", 
            "tool_state": "{\"header\": \"\\\"False\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
            "tool_version": "1.0.3", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "Clusters annotated proximal genes into operons. \nParameter to be set: op_gap. \nGenes separated by a gap smaller than op_gap are clustered \n(suggested value: 10 to 150).", 
            "id": 4, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 2, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Clusterize", 
                    "name": "distance"
                }
            ], 
            "name": "Clusterize", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }, 
                {
                    "name": "outputFileLog", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 547, 
                "top": 297
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Annotation with \"operon\""
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "Clusters overlapping or proximal reads to produce read clusters. \nParameter to be set: clust_gap. \nReads separated by a gap smaller than \nclust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart).", 
            "id": 5, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 3, 
                    "output_name": "output1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Clusterize", 
                    "name": "distance"
                }
            ], 
            "name": "Clusterize", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }, 
                {
                    "name": "outputFileLog", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 496, 
                "top": 596
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Read clusters"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 5, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "Selects read clusters that overlap annotations in the same direction. \nParameter to be set: RNA_gap.\nA read cluster separated from an annotation by a gap smaller than RNA_gap is selected (suggested value: 25).", 
            "id": 6, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 4, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 5, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Compare Overlapping Small Query", 
                    "name": "OptionDistance"
                }
            ], 
            "name": "Compare Overlapping Small Query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 659, 
                "top": 417
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Read clusters overlapping annotation"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "Selects read clusters that form new independent annotations. \nParameter to be set: RNA_gap.\nRead clusters at a distance from existing annotations larger than RNA_gap are selected. Caution: use same RNA_gap value as in previous step!", 
            "id": 7, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 4, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 5, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Compare Overlapping Small Query", 
                    "name": "OptionDistance"
                }
            ], 
            "name": "Compare Overlapping Small Query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 742, 
                "top": 588
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Read clusters not overlapping annotation"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {
            "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be used to extend annotation.", 
            "id": 8, 
            "input_connections": {
                "input1": {
                    "id": 4, 
                    "output_name": "outputFileGff"
                }, 
                "queries_0|input2": {
                    "id": 6, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Concatenate datasets", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 819, 
                "top": 294
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Annotations and read clusters overlapping them"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "cat1", 
            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {
            "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. \nParameter to be set: RNA_gap.\nRead cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!", 
            "id": 9, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 8, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Clusterize", 
                    "name": "distance"
                }
            ], 
            "name": "Clusterize", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }, 
                {
                    "name": "outputFileLog", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1036, 
                "top": 307
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Extended annotation"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {
            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", 
            "id": 10, 
            "input_connections": {
                "input": {
                    "id": 9, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Select", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1232, 
                "top": 319
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Extended annotation without \"exon\" lines"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Grep1", 
            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"exon\\\"\"}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "11": {
            "annotation": "Technical step: orders extended annotations by positions.", 
            "id": 11, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 10, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "collapse reads", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 973, 
                "top": 460
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Ordrered and extended annotation"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "12": {
            "annotation": "Splits extended annotations into UTRs, CDS and/or operon spacers.", 
            "id": 12, 
            "input_connections": {
                "referenciesFile": {
                    "id": 4, 
                    "output_name": "outputFileGff"
                }, 
                "transcriptsFile": {
                    "id": 11, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "splitTranscriptGff", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1221, 
                "top": 456
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "UTRs, CDSs and/or operons"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/splitTranscriptGff/1.0.0", 
            "tool_state": "{\"transcriptsFile\": \"null\", \"__page__\": 0, \"referenciesFile\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "13": {
            "annotation": "Selection of read clusters that are antisense of an extended annotation. \nThis step produces a first list of antisense candidates.", 
            "id": 13, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 11, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 7, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Compare Overlapping Small Query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1155, 
                "top": 617
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "first list of asRNA"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "14": {
            "annotation": "Selection of read clusters that are outside and not in antisense of an extended annotation.\nThis step produces a first list of small RNAs.", 
            "id": 14, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 11, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 7, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Compare Overlapping Small Query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1068, 
                "top": 766
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "first list of sRNA"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "15": {
            "annotation": "Counts reads overlapping UTRs, CDSs and/or operon spacers in order to compute read coverage (with a minimal overlapping region of 10 nt between read and genetic element). Output file of this step can be used to obtain read coverage of 5'UTRs, 3'UTRs, CDSs, or operon spacers.", 
            "id": 15, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 3, 
                    "output_name": "output1"
                }, 
                "formatType|inputFileName1": {
                    "id": 12, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [], 
            "name": "Compare Overlapping Small Reference", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1417, 
                "top": 506
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "UTRs, CDSs and operons (with the number of overlapping reads)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallRef/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"sam\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 4}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"10\\\"}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "16": {
            "annotation": "Filters antisense RNA candidates based on their number of overlapping reads.\nParameter to be set: as_min_reads.\nAntisense RNAs with a number of reads higher than as_min_reads are selected (suggested value: 22).", 
            "id": 16, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 13, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool select by tag", 
                    "name": "OptionMin"
                }
            ], 
            "name": "select by tag", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1461, 
                "top": 663
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "asRNA list modified (filtered on their number of overlapping reads)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "17": {
            "annotation": "Filters sRNA candidates based on their number of overlapping reads.\nParameter to be set: sRNA_min_reads.\nSmall RNAs with a number of reads higher than sRNA_min_reads are selected (suggested value: 12).", 
            "id": 17, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 14, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool select by tag", 
                    "name": "OptionMin"
                }
            ], 
            "name": "select by tag", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1389, 
                "top": 794
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "sRNA list modified (filtered on their number of overlapping reads)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "18": {
            "annotation": "Technical step: coverage computation needs \"nbElements\" tag in place of \"nbOverlaps\".", 
            "id": 18, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 15, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "change tag name", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1696, 
                "top": 541
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "long 5'UTR list modified (tag \"nbElements\")"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeTagName/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"Tag\": \"\\\"nbOverlaps\\\"\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"name\": \"\\\"nbElements\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "19": {
            "annotation": "Clusters proximal antisense RNAs in the same direction.\nParameter to be set: RNA_merge.\nAntisense RNAs located less than RNA_merge apart are merged (suggestion: 50).", 
            "id": 19, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 16, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Clusterize", 
                    "name": "distance"
                }
            ], 
            "name": "Clusterize", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }, 
                {
                    "name": "outputFileLog", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1658, 
                "top": 660
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "asRNA list modified (asRNA clusters)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "20": {
            "annotation": "Clusters proximal small RNAs in the same direction.\nParameter to be set: RNA_merge.\nSmall RNAs located less than RNA_merge apart are merged (suggestion: 50).", 
            "id": 20, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 17, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Clusterize", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }, 
                {
                    "name": "outputFileLog", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1602, 
                "top": 797
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "sRNA list modified (sRNA clusters)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"\\\"50\\\"\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "21": {
            "annotation": "Technical step: extracts 5'UTR features for following steps.", 
            "id": 21, 
            "input_connections": {
                "input1": {
                    "id": 18, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Extract features", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1917, 
                "top": 547
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "first list of long 5'UTR"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Extract_features1", 
            "tool_state": "{\"column_choice\": \"{\\\"col\\\": \\\"2\\\", \\\"__current_case__\\\": 2, \\\"feature\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"utr5\\\"]}}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "22": {
            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", 
            "id": 22, 
            "input_connections": {
                "input": {
                    "id": 19, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Select", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1859, 
                "top": 682
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "asRNA list modified (without \"exon\" lines)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Grep1", 
            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"pattern\": \"\\\"exon\\\"\"}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "23": {
            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", 
            "id": 23, 
            "input_connections": {
                "input": {
                    "id": 20, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Select", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1804, 
                "top": 813
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "sRNA list modified (without \"exon\" lines)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Grep1", 
            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"exon\\\"\"}", 
            "tool_version": "1.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "24": {
            "annotation": "Filters 5'UTR based on their size.\nParameter to be set: 5UTR_min_size.\n5'UTRs larger than 5UTR_min_size are selected (suggestion value: 50).", 
            "id": 24, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 21, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool restrict from size", 
                    "name": "OptionMin"
                }
            ], 
            "name": "restrict from size", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 2132, 
                "top": 570
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "long 5'UTR list modified (filtered on their size)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "25": {
            "annotation": "Filters antisense RNAs based on their size.\nParameter to be set: as_min_size.\nas_min_size is the minimal size for calling an antisense RNA (suggestion: 50).", 
            "id": 25, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 22, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool restrict from size", 
                    "name": "OptionMin"
                }
            ], 
            "name": "restrict from size", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 2085, 
                "top": 691
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "asRNA list modified (filtered on their size)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "26": {
            "annotation": "Filters small RNAs based on their size.\nParameter to be set: sRNA_min_size.\nsRNA_min_size is the minimal size for calling a small RNA (suggestion: 50).", 
            "id": 26, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 23, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool restrict from size", 
                    "name": "OptionMin"
                }
            ], 
            "name": "restrict from size", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 2017, 
                "top": 824
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "sRNA list modified (filtered on their size)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "27": {
            "annotation": "Filters long 5' UTR candidates based on their number of overlapping reads.\nParameter to be set: 5UTR_min_reads.\nLong 5'UTR with a number of reads higher than 5UTR_min_reads is selected (suggested value: 10).", 
            "id": 27, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 24, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool select by tag", 
                    "name": "OptionMin"
                }
            ], 
            "name": "select by tag", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 2344, 
                "top": 577
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "long 5'UTR list modified (filtered on their number of overlapping reads)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "28": {
            "annotation": "Uses an RGB color tag for visualization of antisense RNAs in the Artemis environment.", 
            "id": 28, 
            "input_connections": {
                "referenciesFile": {
                    "id": 25, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "colorGff", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff"
                }
            ], 
            "position": {
                "left": 2321, 
                "top": 715
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "asRNA list modified (annotation color)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"147 112 219\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "29": {
            "annotation": "Uses an RGB color tag for visualization of small RNAs in the Artemis environment.", 
            "id": 29, 
            "input_connections": {
                "referenciesFile": {
                    "id": 26, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "colorGff", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff"
                }
            ], 
            "position": {
                "left": 2247, 
                "top": 838
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "sRNA list modified (annotation color)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"250 128 114\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "30": {
            "annotation": "Uses an RGB color tag for visualization of long 5' UTRs in the Artemis environment.", 
            "id": 30, 
            "input_connections": {
                "referenciesFile": {
                    "id": 27, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "colorGff", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff"
                }
            ], 
            "position": {
                "left": 2525, 
                "top": 610
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "final long 5'UTR list (with the annotation color)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"255 105 180\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "31": {
            "annotation": "Technical step: changes \"transcript\" for \"asRNA\" in the 3rd column.", 
            "id": 31, 
            "input_connections": {
                "inputFile": {
                    "id": 28, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [], 
            "name": "change gff Features", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff"
                }
            ], 
            "position": {
                "left": 2542, 
                "top": 727
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "final asRNA list (with the annotation color)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"transcript\\\"\", \"outputFeature\": \"\\\"asRNA\\\"\", \"inputFile\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "32": {
            "annotation": "Technical step: changes \"transcript\" for \"sRNA\" in the 3rd column.", 
            "id": 32, 
            "input_connections": {
                "inputFile": {
                    "id": 29, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [], 
            "name": "change gff Features", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff"
                }
            ], 
            "position": {
                "left": 2464, 
                "top": 827
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "final sRNA list (with the annotation color)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"transcript\\\"\", \"outputFeature\": \"\\\"sRNA\\\"\", \"inputFile\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}