Mercurial > repos > mcharles > rapsodyn
view rapsodyn/Galaxy-Workflow-Rapsodyn_v1.32.ga @ 11:b7125d07b446 draft
Uploaded
author | mcharles |
---|---|
date | Thu, 14 Aug 2014 09:39:11 -0400 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Rapsodyn v1.32", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "READ1" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 404 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"READ1\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "", "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "READ2" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 489 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"READ2\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "2": { "annotation": "", "id": 2, "input_connections": {}, "inputs": [ { "description": "", "name": "ASSEMBLY" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 574 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"ASSEMBLY\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": {}, "inputs": [ { "description": "", "name": "DUBIOUS POSITION" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 659 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"DUBIOUS POSITION\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "input_file": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "FASTQ Groomer", "outputs": [ { "name": "output_file", "type": "fastqsanger" } ], "position": { "left": 428, "top": 404 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.4", "type": "tool", "user_outputs": [] }, "5": { "annotation": "", "id": 5, "input_connections": { "input_file": { "id": 1, "output_name": "output" } }, "inputs": [], "name": "FASTQ Groomer", "outputs": [ { "name": "output_file", "type": "fastqsanger" } ], "position": { "left": 428, "top": 535 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.4", "type": "tool", "user_outputs": [] }, "6": { "annotation": "", "id": 6, "input_connections": { "input_fasta": { "id": 2, "output_name": "output" } }, "inputs": [], "name": "fastaGroomerForMakeBlastdb", "outputs": [ { "name": "output_fasta", "type": "fasta" } ], "position": { "left": 428, "top": 666 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "fastaGroomerForMakeBlastdb", "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", "tool_version": "0.01", "type": "tool", "user_outputs": [] }, "7": { "annotation": "", "id": 7, "input_connections": { "readtype|input_paired1": { "id": 4, "output_name": "output_file" }, "readtype|input_paired2": { "id": 5, "output_name": "output_file" } }, "inputs": [], "name": "Sickle", "outputs": [ { "name": "output_single", "type": "input" }, { "name": "output_paired1", "type": "fastq" }, { "name": "output_paired2", "type": "fastq" }, { "name": "output_paired_single", "type": "fastq" } ], "position": { "left": 762, "top": 245 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "8": { "annotation": "", "id": 8, "input_connections": { "input_file": { "id": 6, "output_name": "output_fasta" } }, "inputs": [], "name": "NCBI BLAST+ makeblastdb", "outputs": [ { "name": "outfile", "type": "data" } ], "position": { "left": 756, "top": 732 }, "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\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", "tool_version": "0.1.00", "type": "tool", "user_outputs": [] }, "9": { "annotation": "", "id": 9, "input_connections": { "readtype|input_paired1": { "id": 7, "output_name": "output_paired1" }, "readtype|input_paired2": { "id": 7, "output_name": "output_paired2" } }, "inputs": [], "name": "Sickle", "outputs": [ { "name": "output_single", "type": "input" }, { "name": "output_paired1", "type": "fastq" }, { "name": "output_paired2", "type": "fastq" }, { "name": "output_paired_single", "type": "fastq" } ], "position": { "left": 1080, "top": 200 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"qual_threshold\": \"\\\"30\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "10": { "annotation": "", "id": 10, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 9, "output_name": "output_paired1" }, "paired|input2": { "id": 9, "output_name": "output_paired2" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1412, "top": 404 }, "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\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.2.3", "type": "tool", "user_outputs": [] }, "11": { "annotation": "", "id": 11, "input_connections": { "input_sam_file": { "id": 10, "output_name": "output" } }, "inputs": [], "name": "filtersamunique", "outputs": [ { "name": "output_file", "type": "sam" } ], "position": { "left": 1676, "top": 404 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "filtersamunique", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", "tool_version": "0.01", "type": "tool", "user_outputs": [] }, "12": { "annotation": "", "id": 12, "input_connections": { "input1": { "id": 11, "output_name": "output_file" } }, "inputs": [], "name": "Filter SAM or BAM", "outputs": [ { "name": "output1", "type": "sam" } ], "position": { "left": 2004, "top": 404 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1", "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"yes\\\", \\\"skipBits\\\": null, \\\"__current_case__\\\": 1, \\\"reqBits\\\": \\\"0x0002\\\"}\", \"mapq\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.1.1", "type": "tool", "user_outputs": [] }, "13": { "annotation": "", "id": 13, "input_connections": { "source|input1": { "id": 12, "output_name": "output1" }, "source|ref_file": { "id": 2, "output_name": "output" } }, "inputs": [], "name": "SAM-to-BAM", "outputs": [ { "name": "output1", "type": "bam" } ], "position": { "left": 2332, "top": 404 }, "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, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", "tool_version": "1.1.4", "type": "tool", "user_outputs": [] }, "14": { "annotation": "", "id": 14, "input_connections": { "reference_source|input_bams_0|input_bam": { "id": 13, "output_name": "output1" }, "reference_source|ref_file": { "id": 2, "output_name": "output" } }, "inputs": [], "name": "MPileup", "outputs": [ { "name": "output_mpileup", "type": "pileup" }, { "name": "output_log", "type": "txt" } ], "position": { "left": 2560, "top": 404 }, "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, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"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\\\": \\\"30\\\", \\\"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\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "0.0.3", "type": "tool", "user_outputs": [] }, "15": { "annotation": "", "id": 15, "input_connections": { "input_file": { "id": 14, "output_name": "output_mpileup" } }, "inputs": [], "name": "mpileupfilter", "outputs": [ { "name": "output_file", "type": "pileup" } ], "position": { "left": 2886, "top": 404 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "mpileupfilter", "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", "tool_version": "0.05", "type": "tool", "user_outputs": [] }, "16": { "annotation": "", "id": 16, "input_connections": { "input_listA": { "id": 15, "output_name": "output_file" }, "input_listB": { "id": 3, "output_name": "output" } }, "inputs": [], "name": "listfiltering", "outputs": [ { "name": "output_file", "type": "pileup" } ], "position": { "left": 3214, "top": 404 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "listfiltering", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "0.01", "type": "tool", "user_outputs": [] }, "17": { "annotation": "", "id": 17, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 16, "output_name": "output_file" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 3542, "top": 404 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "extractseq", "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "0.03", "type": "tool", "user_outputs": [] }, "18": { "annotation": "", "id": 18, "input_connections": { "db_opts|histdb": { "id": 8, "output_name": "outfile" }, "query": { "id": 17, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 3870, "top": 404 }, "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\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "0.1.00", "type": "tool", "user_outputs": [] }, "19": { "annotation": "", "id": 19, "input_connections": { "input_blastxml_file": { "id": 18, "output_name": "output1" }, "input_variant_file": { "id": 16, "output_name": "output_file" } }, "inputs": [], "name": "mpileupfilteronblastxml", "outputs": [ { "name": "output_file", "type": "pileup" } ], "position": { "left": 4172, "top": 404 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "mpileupfilteronblastxml", "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "0.03", "type": "tool", "user_outputs": [] } } }