Mercurial > repos > clairetn > detrprok_wf

--- a/Galaxy-Workflow-_DetR_Prok_v3__.ga	Sun Mar 24 16:53:14 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1003 +0,0 @@
-{
-    "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": 484.98333740234375
-            },
-            "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": 479.98333740234375
-            },
-            "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": "In box, enter the maximal distance used to cluster reads of same direction for read clusters definition. This distance depends on the deepness of the RNAseq (ex. a value of 0 will cluster only overlapping reads and 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": 496.433349609375,
-                "top": 596.9833374023438
-            },
-            "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": 433.98333740234375
-            },
-            "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! (15 was suggested)",
-            "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": 588.75
-            },
-            "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 extended CDS.",
-            "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": 1036.7333679199219,
-                "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
-            },
-            "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": 460.98333740234375
-            },
-            "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 extended CDS 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": 452.01666259765625
-            },
-            "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 extended CDS. 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": 766.5166320800781
-            },
-            "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\": \"\\\"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": []
-        },
-        "14": {
-            "annotation": "Selection of read clusters that are antisense of the extended CDS. This step produces the first list of antisense candidates.",
-            "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": 618.75
-            },
-            "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\": \"\\\"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": []
-        },
-        "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": 1417.800033569336,
-                "top": 514.9833374023438
-            },
-            "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": 794.5166320800781
-            },
-            "post_job_actions": {},
-            "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": []
-        },
-        "17": {
-            "annotation": "Enter in box the minimum number of reads for calling an antisense RNA (suggested: 10).",
-            "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": 1461.3333740234375,
-                "top": 663.75
-            },
-            "post_job_actions": {},
-            "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": []
-        },
-        "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": 1696.616714477539,
-                "top": 541.2166442871094
-            },
-            "post_job_actions": {},
-            "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": "Enter in box the maximal distance for merging small RNAs located less this distance apart (suggestion: 50).",
-            "id": 19,
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 16,
-                    "output_name": "outputFileGff"
-                }
-            },
-            "inputs": [],
-            "name": "Clusterize",
-            "outputs": [
-                {
-                    "name": "outputFileGff",
-                    "type": "gff3"
-                },
-                {
-                    "name": "outputFileLog",
-                    "type": "txt"
-                }
-            ],
-            "position": {
-                "left": 1602.800033569336,
-                "top": 797.5166320800781
-            },
-            "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\": \"\\\"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": []
-        },
-        "20": {
-            "annotation": "Enter in box the maximal distance for merging antisense RNAs located less this distance apart (suggestion: 50).",
-            "id": 20,
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 17,
-                    "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": 1658.1000366210938,
-                "top": 660.75
-            },
-            "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": []
-        },
-        "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": 1917.5667114257812,
-                "top": 547.9833374023438
-            },
-            "post_job_actions": {},
-            "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": 1804.5667114257812,
-                "top": 813.5166320800781
-            },
-            "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": []
-        },
-        "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": 1859.6666870117188,
-                "top": 682.0666809082031
-            },
-            "post_job_actions": {},
-            "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": []
-        },
-        "24": {
-            "annotation": "Enter minimal size for calling a long 5'UTR (suggestion: 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": 2132.3333740234375,
-                "top": 570.9833374023438
-            },
-            "post_job_actions": {},
-            "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": "Enter minimal size for calling a small 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": 2017.3333740234375,
-                "top": 824.5166320800781
-            },
-            "post_job_actions": {},
-            "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": "Enter minimal size for calling an antisense 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": 2085.6333618164062,
-                "top": 691.75
-            },
-            "post_job_actions": {},
-            "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": "Enter in box the minimum number of reads for calling a long 5' UTR (suggested: 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": 2344.4000244140625,
-                "top": 577.9833374023438
-            },
-            "post_job_actions": {},
-            "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 small 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": 2240.9500732421875,
-                "top": 832.1000061035156
-            },
-            "post_job_actions": {},
-            "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": []
-        },
-        "29": {
-            "annotation": "Uses an RGB color tag for visualization of antisense 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": 2305.9500732421875,
-                "top": 703.1000061035156
-            },
-            "post_job_actions": {},
-            "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": []
-        },
-        "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": 2525.9500732421875,
-                "top": 610.7333374023438
-            },
-            "post_job_actions": {},
-            "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": []
-        }
-    }
-}
\ No newline at end of file