view proteomics_rnaseq_splice_db_workflow.ga @ 1:c2e58e1c045d default tip

Update revisions
author Jim Johnson <jj@umn.edu>
date Mon, 17 Mar 2014 09:52:44 -0500
parents 2f3cb6bae4e9
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from RNAseq data", 
    "format-version": "0.1", 
    "name": "Proteomics Splice DB", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "RNA-Seq left mate pair fastq"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 207, 
                "top": 429
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "RNA-Seq right mate pair fastq"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 205, 
                "top": 639
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"RNA-Seq right mate pair fastq\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Reference Genome FASTA file"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 862, 
                "top": 558
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Reference Genome FASTA file\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {
                "input": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Select first", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 447, 
                "top": 272
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Show beginning1", 
            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"lineNum\": \"\\\"100000\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "input": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Select first", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 445, 
                "top": 737
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Show beginning1", 
            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"lineNum\": \"\\\"100000\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "id": 5, 
            "input_connections": {
                "input1": {
                    "id": 3, 
                    "output_name": "out_file1"
                }, 
                "refGenomeSource|ownFile": {
                    "id": 2, 
                    "output_name": "output"
                }, 
                "singlePaired|input2": {
                    "id": 4, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Tophat for Illumina", 
            "outputs": [
                {
                    "name": "insertions", 
                    "type": "bed"
                }, 
                {
                    "name": "deletions", 
                    "type": "bed"
                }, 
                {
                    "name": "junctions", 
                    "type": "bed"
                }, 
                {
                    "name": "accepted_hits", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 1049, 
                "top": 206
            }, 
            "post_job_actions": {
                "HideDatasetActionaccepted_hits": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "accepted_hits"
                }, 
                "HideDatasetActiondeletions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "deletions"
                }, 
                "HideDatasetActioninsertions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "insertions"
                }, 
                "HideDatasetActionjunctions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "junctions"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", 
            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\", \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.5.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "", 
            "id": 6, 
            "input_connections": {
                "input1": {
                    "id": 3, 
                    "output_name": "out_file1"
                }, 
                "refGenomeSource|ownFile": {
                    "id": 2, 
                    "output_name": "output"
                }, 
                "singlePaired|input2": {
                    "id": 4, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Tophat for Illumina", 
            "outputs": [
                {
                    "name": "insertions", 
                    "type": "bed"
                }, 
                {
                    "name": "deletions", 
                    "type": "bed"
                }, 
                {
                    "name": "junctions", 
                    "type": "bed"
                }, 
                {
                    "name": "accepted_hits", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 1057, 
                "top": 755
            }, 
            "post_job_actions": {
                "HideDatasetActionaccepted_hits": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "accepted_hits"
                }, 
                "HideDatasetActiondeletions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "deletions"
                }, 
                "HideDatasetActioninsertions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "insertions"
                }, 
                "HideDatasetActionjunctions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "junctions"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", 
            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"Yes\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\", \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "1.5.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "", 
            "id": 7, 
            "input_connections": {
                "guided_junctions": {
                    "id": 6, 
                    "output_name": "junctions"
                }, 
                "input_bed": {
                    "id": 5, 
                    "output_name": "junctions"
                }
            }, 
            "inputs": [], 
            "name": "Filter BED on splice junctions", 
            "outputs": [
                {
                    "name": "novel_junctions", 
                    "type": "bed"
                }
            ], 
            "position": {
                "left": 1300, 
                "top": 453
            }, 
            "post_job_actions": {
                "HideDatasetActionnovel_junctions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "novel_junctions"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", 
            "tool_state": "{\"__page__\": 0, \"input_bed\": \"null\", \"__rerun_remap_job_id__\": null, \"leading_bp\": \"\\\"66\\\"\", \"guided_junctions\": \"null\", \"trailing_bp\": \"\\\"66\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", 
            "tool_version": "0.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {
            "annotation": "", 
            "id": 8, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "novel_junctions"
                }, 
                "seq_source|ref_file": {
                    "id": 2, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Extract Genomic DNA", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1499, 
                "top": 668
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "Extract genomic DNA 1", 
            "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"__current_case__\\\": 1}\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", 
            "tool_version": "2.2.3", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {
            "annotation": "", 
            "id": 9, 
            "input_connections": {
                "input": {
                    "id": 8, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "name": "Translate BED Sequences", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1763, 
                "top": 581
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/translate_bed_sequences/translate_bed_sequences/0.0.1", 
            "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"\\\"10\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": \\\"66\\\", \\\"leading_bp\\\": \\\"66\\\", \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", 
            "tool_version": "0.0.1", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}