view Galaxy-Workflow-_DetR_Prok_v3__.ga @ 7:158f0fdfd552 draft

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{
    "a_galaxy_workflow": "true", 
    "annotation": "This workflow aims at identify 3 kinds of ncRNA in prokaryotic sequences. \n\nIt need as entries the alignment file of reads on a genomic sequence (bam format) and the annotation file of the genomic sequence (gff format).", 
    "format-version": "0.1", 
    "name": "\"DetR'Prok_v3''", 
    "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": 160.9000244140625, 
                "top": 353.75
            }, 
            "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": 215.9000244140625, 
                "top": 484.9833526611328
            }, 
            "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": 361.11669921875, 
                "top": 327.0833282470703
            }, 
            "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": 418.666748046875, 
                "top": 479.9833526611328
            }, 
            "post_job_actions": {}, 
            "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": "In box, enter the maximal intergenic distance used for operon definition. This distance depends on the gene density of the organism (try 30 for Escherichia coli, 150 for Vibrio splendidus).", 
            "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": 547.0167236328125, 
                "top": 297.6999969482422
            }, 
            "post_job_actions": {}, 
            "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 overlaping reads of same direction to produce read clusters.", 
            "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": 496.433349609375, 
                "top": 596.9833526611328
            }, 
            "post_job_actions": {}, 
            "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. In box, enter maximal distance to associate a cluster to an annotation (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are 15-nt apart).", 
            "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": 655.2000732421875, 
                "top": 433.9833526611328
            }, 
            "post_job_actions": {}, 
            "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. In box, enter minimal distance between cluster and existing annotations. Caution: use same 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": 742.2000732421875, 
                "top": 588.7500152587891
            }, 
            "post_job_actions": {}, 
            "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 use to define transcription units.", 
            "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": 819.9666748046875, 
                "top": 294.98333740234375
            }, 
            "post_job_actions": {}, 
            "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": "Selects read clusters that overlap annotations in the same direction. In box, enter maximal distance to associate a cluster to an annotation (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are 15-nt apart). This step defines transcription units.", 
            "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": 1036.7333984375, 
                "top": 307.98333740234375
            }, 
            "post_job_actions": {}, 
            "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": 1232.5000610351562, 
                "top": 319.98333740234375
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            "post_job_actions": {}, 
            "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": "List of transcription units (ordered 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": 973.2667236328125, 
                "top": 460.9833526611328
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            "post_job_actions": {}, 
            "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 transcription units 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": 1215.2833862304688, 
                "top": 452.0166778564453
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            "post_job_actions": {}, 
            "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 outside and not in antisense of transcription units. This step produces the first list of small RNAs.", 
            "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": 1068.0333862304688, 
                "top": 766.5166778564453
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            "post_job_actions": {}, 
            "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\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"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 antisense of the transcription units.", 
            "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": 1170.0333862304688, 
                "top": 618.7500152587891
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            "post_job_actions": {}, 
            "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\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"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": "Count 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": 1417.800048828125, 
                "top": 514.9833526611328
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            "post_job_actions": {}, 
            "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": "Enter in box the minimum number of reads for calling an sRNA (suggested: 10).", 
            "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": 1389.1000366210938, 
                "top": 794.5166778564453
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