view rapsodyn/Galaxy-Workflow-rapsosnp_v1.20.ga @ 9:0e7c6fe60646 draft

Uploaded
author mcharles
date Mon, 20 Oct 2014 05:58:31 -0400
parents d857538d9fea
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "rapsosnp v1.20", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "ASSEMBLY"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 221
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"ASSEMBLY\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "READ1"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 306.76666259765625
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"READ1\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "READ2"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 392.5333251953125
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"READ2\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "id": 3, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "DUBIOUS"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 478.29998779296875
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"DUBIOUS\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "id": 4, 
            "input_connections": {
                "input_fasta": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "fastaGroomerForMakeBlastdb", 
            "outputs": [
                {
                    "name": "output_fasta", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 427.76666259765625, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "fastaGroomerForMakeBlastdb", 
            "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "1.00", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "id": 5, 
            "input_connections": {
                "input_read1_file": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "input_read2_file": {
                    "id": 2, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "PrepareFastqLight", 
            "outputs": [
                {
                    "name": "output_read1_file", 
                    "type": "fastqsanger"
                }, 
                {
                    "name": "output_read2_file", 
                    "type": "fastqsanger"
                }, 
                {
                    "name": "log_file", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 427.76666259765625, 
                "top": 351.76666259765625
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "PrepareFastqLight", 
            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
            "tool_version": "1.03", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "", 
            "id": 6, 
            "input_connections": {
                "input_file": {
                    "id": 4, 
                    "output_name": "output_fasta"
                }
            }, 
            "inputs": [], 
            "name": "NCBI BLAST+ makeblastdb", 
            "outputs": [
                {
                    "name": "outfile", 
                    "type": "data"
                }
            ], 
            "position": {
                "left": 755.5333251953125, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", 
            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 
            "tool_version": "0.1.00", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "", 
            "id": 7, 
            "input_connections": {
                "genomeSource|ownFile": {
                    "id": 0, 
                    "output_name": "output"
                }, 
                "paired|input1": {
                    "id": 5, 
                    "output_name": "output_read1_file"
                }, 
                "paired|input2": {
                    "id": 5, 
                    "output_name": "output_read2_file"
                }
            }, 
            "inputs": [], 
            "name": "Map with BWA for Illumina", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "sam"
                }
            ], 
            "position": {
                "left": 755.5333251953125, 
                "top": 378.76666259765625
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", 
            "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}", 
            "tool_version": "1.2.3", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {
            "annotation": "", 
            "id": 8, 
            "input_connections": {
                "input_sam_file": {
                    "id": 7, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "filtersam_mapped_and_unique", 
            "outputs": [
                {
                    "name": "output_sam_file", 
                    "type": "sam"
                }, 
                {
                    "name": "log_file", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1083.300048828125, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "filtersam_mapped_and_unique", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}", 
            "tool_version": "1.01", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {
            "annotation": "", 
            "id": 9, 
            "input_connections": {
                "source|input1": {
                    "id": 8, 
                    "output_name": "output_sam_file"
                }, 
                "source|ref_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "SAM-to-BAM", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 1411.066650390625, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "1.1.4", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {
            "annotation": "", 
            "id": 10, 
            "input_connections": {
                "reference_source|input_bams_0|input_bam": {
                    "id": 9, 
                    "output_name": "output1"
                }, 
                "reference_source|ref_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "MPileup", 
            "outputs": [
                {
                    "name": "output_mpileup", 
                    "type": "pileup"
                }, 
                {
                    "name": "output_log", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1638.8333740234375, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
            "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"0\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}", 
            "tool_version": "0.0.3", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "11": {
            "annotation": "", 
            "id": 11, 
            "input_connections": {
                "input_pileup_file": {
                    "id": 10, 
                    "output_name": "output_mpileup"
                }
            }, 
            "inputs": [], 
            "name": "PileupVariant", 
            "outputs": [
                {
                    "name": "output_pileup_file", 
                    "type": "pileup"
                }, 
                {
                    "name": "log_file", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1964.60009765625, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "PileupVariant", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_pileup_file\": \"null\"}", 
            "tool_version": "1.01", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "12": {
            "annotation": "", 
            "id": 12, 
            "input_connections": {
                "input_list1": {
                    "id": 11, 
                    "output_name": "output_pileup_file"
                }, 
                "input_list2": {
                    "id": 3, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "listfiltering", 
            "outputs": [
                {
                    "name": "output_file", 
                    "type": "pileup"
                }, 
                {
                    "name": "log_file", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 2292.36669921875, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "listfiltering", 
            "tool_state": "{\"__page__\": 0, \"input_list2\": \"null\", \"input_list1\": \"null\", \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"type\": \"\\\"specific\\\"\"}", 
            "tool_version": "1.01", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "13": {
            "annotation": "", 
            "id": 13, 
            "input_connections": {
                "input_assembly_file": {
                    "id": 0, 
                    "output_name": "output"
                }, 
                "input_variant_file": {
                    "id": 12, 
                    "output_name": "output_file"
                }
            }, 
            "inputs": [], 
            "name": "extractseq", 
            "outputs": [
                {
                    "name": "output_file", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 2561.13330078125, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "extractseq", 
            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}", 
            "tool_version": "1.01", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "14": {
            "annotation": "", 
            "id": 14, 
            "input_connections": {
                "db_opts|histdb": {
                    "id": 6, 
                    "output_name": "outfile"
                }, 
                "query": {
                    "id": 13, 
                    "output_name": "output_file"
                }
            }, 
            "inputs": [], 
            "name": "NCBI BLAST+ blastn", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 2888.89990234375, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", 
            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}", 
            "tool_version": "0.1.00", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "15": {
            "annotation": "", 
            "id": 15, 
            "input_connections": {
                "input_blast_file": {
                    "id": 14, 
                    "output_name": "output1"
                }, 
                "input_variant_file": {
                    "id": 12, 
                    "output_name": "output_file"
                }
            }, 
            "inputs": [], 
            "name": "ParseBlastForUniqueMatch", 
            "outputs": [
                {
                    "name": "output_variant_file", 
                    "type": "pileup"
                }, 
                {
                    "name": "log_file", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 3190.666748046875, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "ParseBlastForUniqueMatch", 
            "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}", 
            "tool_version": "1.01", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "16": {
            "annotation": "", 
            "id": 16, 
            "input_connections": {
                "input_file": {
                    "id": 15, 
                    "output_name": "output_variant_file"
                }
            }, 
            "inputs": [], 
            "name": "mpileupfilterandstat", 
            "outputs": [
                {
                    "name": "output_file", 
                    "type": "pileup"
                }, 
                {
                    "name": "log_file", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 3518.433349609375, 
                "top": 221
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "mpileupfilterandstat", 
            "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"4\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"20\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"4\\\", \\\"stat_max_depth_min\\\": \\\"200\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.2\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.0\\\"\", \"min_depth\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"500\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
            "tool_version": "1.00", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "17": {
            "annotation": "", 
            "id": 17, 
            "input_connections": {
                "input_files": [
                    {
                        "id": 5, 
                        "output_name": "log_file"
                    }, 
                    {
                        "id": 8, 
                        "output_name": "log_file"
                    }, 
                    {
                        "id": 11, 
                        "output_name": "log_file"
                    }, 
                    {
                        "id": 12, 
                        "output_name": "log_file"
                    }, 
                    {
                        "id": 15, 
                        "output_name": "log_file"
                    }, 
                    {
                        "id": 16, 
                        "output_name": "log_file"
                    }
                ]
            }, 
            "inputs": [], 
            "name": "MergeMultiFile", 
            "outputs": [
                {
                    "name": "output_file", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 3846.2001953125, 
                "top": 221
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutput_file": {
                    "action_arguments": {
                        "newname": "LOGS"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "MergeMultiFile", 
            "tool_state": "{\"out_format\": \"\\\"txt\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}", 
            "tool_version": "1.00", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}