Mercurial > repos > mcharles > rapsosnp
view rapsodyn/Galaxy-Workflow-rapsosnp_v1.5.ga @ 15:56d328bce3a7 draft default tip
Uploaded
author | mcharles |
---|---|
date | Thu, 29 Jan 2015 08:54:06 -0500 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "rapsosnp v1.5", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "READ1" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 805 }, "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": 203, "top": 905 }, "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": 3465, "top": 399 }, "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": "EXCLUDED POSITIONS" } ], "name": "Input dataset", "outputs": [], "position": { "left": 3421.25, "top": 1189.75 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"EXCLUDED POSITIONS\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "input_file": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "SplitFileUpTo10x", "outputs": [ { "name": "output_file1", "type": "txt" }, { "name": "output_file2", "type": "txt" }, { "name": "output_file3", "type": "txt" }, { "name": "output_file4", "type": "txt" }, { "name": "output_file5", "type": "txt" }, { "name": "output_file6", "type": "txt" }, { "name": "output_file7", "type": "txt" }, { "name": "output_file8", "type": "txt" }, { "name": "output_file9", "type": "txt" }, { "name": "output_file10", "type": "txt" } ], "position": { "left": 389, "top": 644 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "SplitFileUpTo10x", "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"file_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", "tool_version": "1.00", "type": "tool", "user_outputs": [] }, "5": { "annotation": "", "id": 5, "input_connections": { "input_file": { "id": 1, "output_name": "output" } }, "inputs": [], "name": "SplitFileUpTo10x", "outputs": [ { "name": "output_file1", "type": "txt" }, { "name": "output_file2", "type": "txt" }, { "name": "output_file3", "type": "txt" }, { "name": "output_file4", "type": "txt" }, { "name": "output_file5", "type": "txt" }, { "name": "output_file6", "type": "txt" }, { "name": "output_file7", "type": "txt" }, { "name": "output_file8", "type": "txt" }, { "name": "output_file9", "type": "txt" }, { "name": "output_file10", "type": "txt" } ], "position": { "left": 392, "top": 1175 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "SplitFileUpTo10x", "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"file_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", "tool_version": "1.00", "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": 4557.25, "top": 278.75 }, "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": [] }, "7": { "annotation": "", "id": 7, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file1" }, "input_read2_file": { "id": 5, "output_name": "output_file1" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 718.75, "top": 626.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "8": { "annotation": "", "id": 8, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file2" }, "input_read2_file": { "id": 5, "output_name": "output_file2" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 722.75, "top": 839.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "9": { "annotation": "", "id": 9, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file6" }, "input_read2_file": { "id": 5, "output_name": "output_file6" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1028.75, "top": 624.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "10": { "annotation": "", "id": 10, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file3" }, "input_read2_file": { "id": 5, "output_name": "output_file3" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 721.75, "top": 1059.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "11": { "annotation": "", "id": 11, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file7" }, "input_read2_file": { "id": 5, "output_name": "output_file7" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1033.75, "top": 844.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "12": { "annotation": "", "id": 12, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file4" }, "input_read2_file": { "id": 5, "output_name": "output_file4" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 723.75, "top": 1274.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "13": { "annotation": "", "id": 13, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file8" }, "input_read2_file": { "id": 5, "output_name": "output_file8" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1033.75, "top": 1068.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "14": { "annotation": "", "id": 14, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file9" }, "input_read2_file": { "id": 5, "output_name": "output_file9" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1037.75, "top": 1281.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "15": { "annotation": "", "id": 15, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file5" }, "input_read2_file": { "id": 5, "output_name": "output_file5" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 725.75, "top": 1495.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "16": { "annotation": "", "id": 16, "input_connections": { "input_read1_file": { "id": 4, "output_name": "output_file10" }, "input_read2_file": { "id": 5, "output_name": "output_file10" } }, "inputs": [], "name": "PrepareFastqLight", "outputs": [ { "name": "output_read1_file", "type": "fastqsanger" }, { "name": "output_read2_file", "type": "fastqsanger" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1039.75, "top": 1496.25 }, "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": "1.11", "type": "tool", "user_outputs": [] }, "17": { "annotation": "", "id": 17, "input_connections": { "input_file": { "id": 6, "output_name": "output_fasta" } }, "inputs": [], "name": "NCBI BLAST+ makeblastdb", "outputs": [ { "name": "outfile", "type": "data" } ], "position": { "left": 4974.25, "top": 271.75 }, "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": [] }, "18": { "annotation": "", "id": 18, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 7, "output_name": "output_read1_file" }, "paired|input2": { "id": 7, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1378, "top": 625 }, "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": [] }, "19": { "annotation": "", "id": 19, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 8, "output_name": "output_read1_file" }, "paired|input2": { "id": 8, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1391, "top": 852 }, "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": [] }, "20": { "annotation": "", "id": 20, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 9, "output_name": "output_read1_file" }, "paired|input2": { "id": 9, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1660, "top": 622 }, "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": [] }, "21": { "annotation": "", "id": 21, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 10, "output_name": "output_read1_file" }, "paired|input2": { "id": 10, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1383, "top": 1060 }, "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": [] }, "22": { "annotation": "", "id": 22, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 11, "output_name": "output_read1_file" }, "paired|input2": { "id": 11, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1663, "top": 845 }, "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": [] }, "23": { "annotation": "", "id": 23, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 12, "output_name": "output_read1_file" }, "paired|input2": { "id": 12, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1391, "top": 1277 }, "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": [] }, "24": { "annotation": "", "id": 24, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 13, "output_name": "output_read1_file" }, "paired|input2": { "id": 13, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1663, "top": 1059 }, "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": [] }, "25": { "annotation": "", "id": 25, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 14, "output_name": "output_read1_file" }, "paired|input2": { "id": 14, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1671, "top": 1281 }, "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": [] }, "26": { "annotation": "", "id": 26, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 15, "output_name": "output_read1_file" }, "paired|input2": { "id": 15, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1397, "top": 1497 }, "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": [] }, "27": { "annotation": "", "id": 27, "input_connections": { "genomeSource|ownFile": { "id": 2, "output_name": "output" }, "paired|input1": { "id": 16, "output_name": "output_read1_file" }, "paired|input2": { "id": 16, "output_name": "output_read2_file" } }, "inputs": [], "name": "Map with BWA for Illumina", "outputs": [ { "name": "output", "type": "sam" } ], "position": { "left": 1667, "top": 1494 }, "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": [] }, "28": { "annotation": "", "id": 28, "input_connections": { "input_sam_file": { "id": 18, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1984.75, "top": 621.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "29": { "annotation": "", "id": 29, "input_connections": { "input_sam_file": { "id": 19, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1986.75, "top": 841.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "30": { "annotation": "", "id": 30, "input_connections": { "input_sam_file": { "id": 20, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 2287.75, "top": 623.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "31": { "annotation": "", "id": 31, "input_connections": { "input_sam_file": { "id": 21, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1990.75, "top": 1046.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "32": { "annotation": "", "id": 32, "input_connections": { "input_sam_file": { "id": 22, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 2289.75, "top": 840.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "33": { "annotation": "", "id": 33, "input_connections": { "input_sam_file": { "id": 23, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1991.75, "top": 1275.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "34": { "annotation": "", "id": 34, "input_connections": { "input_sam_file": { "id": 24, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 2293.75, "top": 1041.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "35": { "annotation": "", "id": 35, "input_connections": { "input_sam_file": { "id": 25, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 2298.75, "top": 1272.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "36": { "annotation": "", "id": 36, "input_connections": { "input_sam_file": { "id": 26, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 1991.75, "top": 1490.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "37": { "annotation": "", "id": 37, "input_connections": { "input_sam_file": { "id": 27, "output_name": "output" } }, "inputs": [], "name": "filtersam_mapped_and_unique", "outputs": [ { "name": "output_sam_file", "type": "sam" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 2308.75, "top": 1488.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "38": { "annotation": "", "id": 38, "input_connections": { "input_files": [ { "id": 37, "output_name": "output_sam_file" }, { "id": 36, "output_name": "output_sam_file" }, { "id": 35, "output_name": "output_sam_file" }, { "id": 34, "output_name": "output_sam_file" }, { "id": 33, "output_name": "output_sam_file" }, { "id": 32, "output_name": "output_sam_file" }, { "id": 31, "output_name": "output_sam_file" }, { "id": 30, "output_name": "output_sam_file" }, { "id": 29, "output_name": "output_sam_file" }, { "id": 28, "output_name": "output_sam_file" } ] }, "inputs": [], "name": "MergeSamFiles", "outputs": [ { "name": "output_file", "type": "sam" } ], "position": { "left": 2785.25, "top": 992.75 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "MergeSamFiles", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}", "tool_version": "1.00", "type": "tool", "user_outputs": [] }, "39": { "annotation": "", "id": 39, "input_connections": { "source|input1": { "id": 38, "output_name": "output_file" }, "source|ref_file": { "id": 2, "output_name": "output" } }, "inputs": [], "name": "SAM-to-BAM", "outputs": [ { "name": "output1", "type": "bam" } ], "position": { "left": 3099.25, "top": 993.75 }, "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": [] }, "40": { "annotation": "", "id": 40, "input_connections": { "reference_source|input_bams_0|input_bam": { "id": 39, "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": 3313.25, "top": 935.75 }, "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": [] }, "41": { "annotation": "", "id": 41, "input_connections": { "exclude|input_exclusion_file": { "id": 3, "output_name": "output" }, "input_pileup_file": { "id": 40, "output_name": "output_mpileup" } }, "inputs": [], "name": "PileupVariant", "outputs": [ { "name": "output_pileup_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 3612.25, "top": 944.75 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "PileupVariant", "tool_state": "{\"exclude\": \"{\\\"do\\\": \\\"YES\\\", \\\"input_exclusion_file\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"input_pileup_file\": \"null\", \"__page__\": 0}", "tool_version": "1.10", "type": "tool", "user_outputs": [] }, "42": { "annotation": "", "id": 42, "input_connections": { "input_file": { "id": 41, "output_name": "output_pileup_file" } }, "inputs": [], "name": "SplitFileUpTo10x", "outputs": [ { "name": "output_file1", "type": "txt" }, { "name": "output_file2", "type": "txt" }, { "name": "output_file3", "type": "txt" }, { "name": "output_file4", "type": "txt" }, { "name": "output_file5", "type": "txt" }, { "name": "output_file6", "type": "txt" }, { "name": "output_file7", "type": "txt" }, { "name": "output_file8", "type": "txt" }, { "name": "output_file9", "type": "txt" }, { "name": "output_file10", "type": "txt" } ], "position": { "left": 3899.25, "top": 723.75 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "SplitFileUpTo10x", "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"file_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", "tool_version": "1.00", "type": "tool", "user_outputs": [] }, "43": { "annotation": "", "id": 43, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file1" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4231.25, "top": 470.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "44": { "annotation": "", "id": 44, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file2" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4234.25, "top": 663.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "45": { "annotation": "", "id": 45, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file3" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4240.25, "top": 863.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "46": { "annotation": "", "id": 46, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file4" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4246.25, "top": 1097.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "47": { "annotation": "", "id": 47, "input_connections": { "input_variant_file": { "id": 42, "output_name": "output_file5" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4244.25, "top": 1330.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "48": { "annotation": "", "id": 48, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file6" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4569.25, "top": 472.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "49": { "annotation": "", "id": 49, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file7" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4572.25, "top": 658.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "50": { "annotation": "", "id": 50, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file8" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4577.25, "top": 871.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "51": { "annotation": "", "id": 51, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file9" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4582.25, "top": 1094.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "52": { "annotation": "", "id": 52, "input_connections": { "input_assembly_file": { "id": 2, "output_name": "output" }, "input_variant_file": { "id": 42, "output_name": "output_file10" } }, "inputs": [], "name": "extractseq", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 4585.25, "top": 1330.75 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "53": { "annotation": "", "id": 53, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 43, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 5000.75, "top": 478.75 }, "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, \"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": [] }, "54": { "annotation": "", "id": 54, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 44, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 4996.75, "top": 682.75 }, "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, \"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": [] }, "55": { "annotation": "", "id": 55, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 45, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 4997.75, "top": 873.75 }, "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, \"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": [] }, "56": { "annotation": "", "id": 56, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 46, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 4990.75, "top": 1090.75 }, "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, \"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": [] }, "57": { "annotation": "", "id": 57, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 47, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 5000.75, "top": 1337.75 }, "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, \"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": [] }, "58": { "annotation": "", "id": 58, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 48, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 5279.75, "top": 471.75 }, "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, \"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": [] }, "59": { "annotation": "", "id": 59, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 49, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 5288.75, "top": 677.75 }, "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, \"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": [] }, "60": { "annotation": "", "id": 60, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 50, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 5297.75, "top": 874.75 }, "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, \"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": [] }, "61": { "annotation": "", "id": 61, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 51, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 5304.75, "top": 1091.75 }, "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, \"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": [] }, "62": { "annotation": "", "id": 62, "input_connections": { "db_opts|histdb": { "id": 17, "output_name": "outfile" }, "query": { "id": 52, "output_name": "output_file" } }, "inputs": [], "name": "NCBI BLAST+ blastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 5309.75, "top": 1328.75 }, "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, \"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": [] }, "63": { "annotation": "", "id": 63, "input_connections": { "input_blast_file": { "id": 53, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file1" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5611.89990234375, "top": 356.3000030517578 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "64": { "annotation": "", "id": 64, "input_connections": { "input_blast_file": { "id": 54, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file2" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5608.89990234375, "top": 598.3000030517578 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "65": { "annotation": "", "id": 65, "input_connections": { "input_blast_file": { "id": 55, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file3" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5614.89990234375, "top": 837.2999877929688 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "66": { "annotation": "", "id": 66, "input_connections": { "input_blast_file": { "id": 56, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file4" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5613.89990234375, "top": 1074.2999877929688 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "67": { "annotation": "", "id": 67, "input_connections": { "input_blast_file": { "id": 57, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file5" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5619.89990234375, "top": 1313.2999877929688 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "68": { "annotation": "", "id": 68, "input_connections": { "input_blast_file": { "id": 58, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file6" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5937.89990234375, "top": 354.3000030517578 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "69": { "annotation": "", "id": 69, "input_connections": { "input_blast_file": { "id": 59, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file7" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5939.89990234375, "top": 596.3000030517578 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "70": { "annotation": "", "id": 70, "input_connections": { "input_blast_file": { "id": 60, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file8" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5942.89990234375, "top": 834.2999877929688 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "71": { "annotation": "", "id": 71, "input_connections": { "input_blast_file": { "id": 61, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file9" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5943.89990234375, "top": 1063.2999877929688 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "72": { "annotation": "", "id": 72, "input_connections": { "input_blast_file": { "id": 62, "output_name": "output1" }, "input_variant_file": { "id": 42, "output_name": "output_file10" } }, "inputs": [], "name": "ParseBlastForUniqueMatch", "outputs": [ { "name": "output_variant_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 5937.89990234375, "top": 1314.2999877929688 }, "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": "1.10", "type": "tool", "user_outputs": [] }, "73": { "annotation": "", "id": 73, "input_connections": { "input_files": [ { "id": 72, "output_name": "output_variant_file" }, { "id": 71, "output_name": "output_variant_file" }, { "id": 70, "output_name": "output_variant_file" }, { "id": 69, "output_name": "output_variant_file" }, { "id": 68, "output_name": "output_variant_file" }, { "id": 67, "output_name": "output_variant_file" }, { "id": 66, "output_name": "output_variant_file" }, { "id": 65, "output_name": "output_variant_file" }, { "id": 64, "output_name": "output_variant_file" }, { "id": 63, "output_name": "output_variant_file" } ] }, "inputs": [], "name": "MergeMultiFile", "outputs": [ { "name": "output_file", "type": "txt" } ], "position": { "left": 6432.89990234375, "top": 801.3000030517578 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "MergeMultiFile", "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}", "tool_version": "1.00", "type": "tool", "user_outputs": [] }, "74": { "annotation": "", "id": 74, "input_connections": { "input_file": { "id": 73, "output_name": "output_file" } }, "inputs": [], "name": "mpileupfilterandstat", "outputs": [ { "name": "output_file", "type": "pileup" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 6806.39990234375, "top": 829.3000030517578 }, "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\\\": \\\"500\\\", \\\"stat_min_depth_max\\\": \\\"20\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"4\\\", \\\"stat_max_depth_min\\\": \\\"250\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"250\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.1\\\", \\\"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": [] }, "75": { "annotation": "", "id": 75, "input_connections": { "input_log_files": [ { "id": 74, "output_name": "log_file" }, { "id": 72, "output_name": "log_file" }, { "id": 71, "output_name": "log_file" }, { "id": 70, "output_name": "log_file" }, { "id": 69, "output_name": "log_file" }, { "id": 68, "output_name": "log_file" }, { "id": 67, "output_name": "log_file" }, { "id": 66, "output_name": "log_file" }, { "id": 65, "output_name": "log_file" }, { "id": 64, "output_name": "log_file" }, { "id": 63, "output_name": "log_file" }, { "id": 41, "output_name": "log_file" }, { "id": 37, "output_name": "log_file" }, { "id": 36, "output_name": "log_file" }, { "id": 35, "output_name": "log_file" }, { "id": 34, "output_name": "log_file" }, { "id": 33, "output_name": "log_file" }, { "id": 32, "output_name": "log_file" }, { "id": 31, "output_name": "log_file" }, { "id": 30, "output_name": "log_file" }, { "id": 29, "output_name": "log_file" }, { "id": 28, "output_name": "log_file" }, { "id": 16, "output_name": "log_file" }, { "id": 15, "output_name": "log_file" }, { "id": 14, "output_name": "log_file" }, { "id": 13, "output_name": "log_file" }, { "id": 12, "output_name": "log_file" }, { "id": 11, "output_name": "log_file" }, { "id": 10, "output_name": "log_file" }, { "id": 9, "output_name": "log_file" }, { "id": 8, "output_name": "log_file" }, { "id": 7, "output_name": "log_file" } ] }, "inputs": [], "name": "MergeLogFiles", "outputs": [ { "name": "output_file", "type": "txt" } ], "position": { "left": 7106.89990234375, "top": 1007.2999877929688 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "MergeLogFiles", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_log_files\": \"null\"}", "tool_version": "1.00", "type": "tool", "user_outputs": [] } } }