Mercurial > repos > mcharles > rapsosnp
diff rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_2x.ga @ 1:7f36bd129321 draft
Uploaded
| author | mcharles |
|---|---|
| date | Wed, 10 Sep 2014 10:24:01 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_2x.ga Wed Sep 10 10:24:01 2014 -0400 @@ -0,0 +1,1014 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "rapsosnp v1.15 - 2x", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "ASSEMBLY" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200.000244140625, + "top": 211 + }, + "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": 200.000244140625, + "top": 296 + }, + "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": 200.000244140625, + "top": 381 + }, + "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": 200.000244140625, + "top": 466 + }, + "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": 428.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "fastaGroomerForMakeBlastdb", + "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "name": "SplitFile2x", + "outputs": [ + { + "name": "output_file1", + "type": "txt" + }, + { + "name": "output_file2", + "type": "txt" + } + ], + "position": { + "left": 428.000244140625, + "top": 342 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "SplitFile2x", + "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "input_file": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "SplitFile2x", + "outputs": [ + { + "name": "output_file1", + "type": "txt" + }, + { + "name": "output_file2", + "type": "txt" + } + ], + "position": { + "left": 428.000244140625, + "top": 534 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "SplitFile2x", + "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "input_file": { + "id": 4, + "output_name": "output_fasta" + } + }, + "inputs": [], + "name": "NCBI BLAST+ makeblastdb", + "outputs": [ + { + "name": "outfile", + "type": "data" + } + ], + "position": { + "left": 756.000244140625, + "top": 615.0000305175781 + }, + "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": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "input_read1_file": { + "id": 5, + "output_name": "output_file1" + }, + "input_read2_file": { + "id": 6, + "output_name": "output_file1" + } + }, + "inputs": [], + "name": "PrepareFastqLight", + "outputs": [ + { + "name": "output_read1_file", + "type": "fastqsanger" + }, + { + "name": "output_read2_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 756.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "PrepareFastqLight", + "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "input_read1_file": { + "id": 5, + "output_name": "output_file2" + }, + "input_read2_file": { + "id": 6, + "output_name": "output_file2" + } + }, + "inputs": [], + "name": "PrepareFastqLight", + "outputs": [ + { + "name": "output_read1_file", + "type": "fastqsanger" + }, + { + "name": "output_read2_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 756.000244140625, + "top": 413 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "PrepareFastqLight", + "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "", + "id": 10, + "input_connections": { + "genomeSource|ownFile": { + "id": 0, + "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": 1084.000244140625, + "top": 211 + }, + "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/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.2.3", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "genomeSource|ownFile": { + "id": 0, + "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": 1084.000244140625, + "top": 396 + }, + "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/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.2.3", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": { + "input_sam_file": { + "id": 10, + "output_name": "output" + } + }, + "inputs": [], + "name": "filtersam_mapped_and_unique", + "outputs": [ + { + "name": "output_file", + "type": "sam" + } + ], + "position": { + "left": 1348.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "filtersam_mapped_and_unique", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "input_sam_file": { + "id": 11, + "output_name": "output" + } + }, + "inputs": [], + "name": "filtersam_mapped_and_unique", + "outputs": [ + { + "name": "output_file", + "type": "sam" + } + ], + "position": { + "left": 1348.000244140625, + "top": 342 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "filtersam_mapped_and_unique", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "", + "id": 14, + "input_connections": { + "source|input1": { + "id": 12, + "output_name": "output_file" + }, + "source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1676.000244140625, + "top": 211 + }, + "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/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", + "tool_version": "1.1.4", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "", + "id": 15, + "input_connections": { + "source|input1": { + "id": 13, + "output_name": "output_file" + }, + "source|ref_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 1676.000244140625, + "top": 352 + }, + "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/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", + "tool_version": "1.1.4", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "input1": { + "id": 14, + "output_name": "output1" + }, + "input2": { + "id": 15, + "output_name": "output1" + } + }, + "inputs": [], + "name": "Merge BAM Files", + "outputs": [ + { + "name": "output1", + "type": "bam" + }, + { + "name": "outlog", + "type": "txt" + } + ], + "position": { + "left": 1904.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2", + "tool_state": "{\"input2\": \"null\", \"inputs\": \"[]\", \"input1\": \"null\", \"title\": \"\\\"merge bam\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mergeSD\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.1.2", + "type": "tool", + "user_outputs": [] + }, + "17": { + "annotation": "", + "id": 17, + "input_connections": { + "reference_source|input_bams_0|input_bam": { + "id": 16, + "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": 2132.000244140625, + "top": 211 + }, + "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/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.0.3", + "type": "tool", + "user_outputs": [] + }, + "18": { + "annotation": "", + "id": 18, + "input_connections": { + "input_file": { + "id": 17, + "output_name": "output_mpileup" + } + }, + "inputs": [], + "name": "PileupVariant", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 2458.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "PileupVariant", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "19": { + "annotation": "", + "id": 19, + "input_connections": { + "input_listA": { + "id": 18, + "output_name": "output_file" + }, + "input_listB": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "name": "listfiltering", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 2786.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "listfiltering", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "20": { + "annotation": "", + "id": 20, + "input_connections": { + "input_file": { + "id": 19, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "SplitFile2x", + "outputs": [ + { + "name": "output_file1", + "type": "txt" + }, + { + "name": "output_file2", + "type": "txt" + } + ], + "position": { + "left": 3114.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "SplitFile2x", + "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "21": { + "annotation": "", + "id": 21, + "input_connections": { + "input_assembly_file": { + "id": 0, + "output_name": "output" + }, + "input_variant_file": { + "id": 20, + "output_name": "output_file1" + } + }, + "inputs": [], + "name": "extractseq", + "outputs": [ + { + "name": "output_file", + "type": "fasta" + } + ], + "position": { + "left": 3442.000244140625, + "top": 211 + }, + "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": "0.03", + "type": "tool", + "user_outputs": [] + }, + "22": { + "annotation": "", + "id": 22, + "input_connections": { + "input_assembly_file": { + "id": 0, + "output_name": "output" + }, + "input_variant_file": { + "id": 20, + "output_name": "output_file2" + } + }, + "inputs": [], + "name": "extractseq", + "outputs": [ + { + "name": "output_file", + "type": "fasta" + } + ], + "position": { + "left": 3442.000244140625, + "top": 386 + }, + "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": "0.03", + "type": "tool", + "user_outputs": [] + }, + "23": { + "annotation": "", + "id": 23, + "input_connections": { + "db_opts|histdb": { + "id": 7, + "output_name": "outfile" + }, + "query": { + "id": 21, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "NCBI BLAST+ blastn", + "outputs": [ + { + "name": "output1", + "type": "tabular" + } + ], + "position": { + "left": 3770.000244140625, + "top": 211 + }, + "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": [] + }, + "24": { + "annotation": "", + "id": 24, + "input_connections": { + "db_opts|histdb": { + "id": 7, + "output_name": "outfile" + }, + "query": { + "id": 22, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "NCBI BLAST+ blastn", + "outputs": [ + { + "name": "output1", + "type": "tabular" + } + ], + "position": { + "left": 3770.000244140625, + "top": 352 + }, + "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": [] + }, + "25": { + "annotation": "", + "id": 25, + "input_connections": { + "input_blast_file": { + "id": 23, + "output_name": "output1" + }, + "input_variant_file": { + "id": 20, + "output_name": "output_file1" + } + }, + "inputs": [], + "name": "ParseBlastForUniqueMatch", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 4072.000228881836, + "top": 211 + }, + "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": "0.01", + "type": "tool", + "user_outputs": [] + }, + "26": { + "annotation": "", + "id": 26, + "input_connections": { + "input_blast_file": { + "id": 24, + "output_name": "output1" + }, + "input_variant_file": { + "id": 20, + "output_name": "output_file2" + } + }, + "inputs": [], + "name": "ParseBlastForUniqueMatch", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 4072.000228881836, + "top": 420 + }, + "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": "0.01", + "type": "tool", + "user_outputs": [] + }, + "27": { + "annotation": "", + "id": 27, + "input_connections": { + "input_file1": { + "id": 25, + "output_name": "output_file" + }, + "input_file2": { + "id": 26, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "MergeFile2x", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 4400.000228881836, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "MergeFile2x", + "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file1\": \"null\", \"input_file2\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "28": { + "annotation": "", + "id": 28, + "input_connections": { + "input_file": { + "id": 27, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "mpileupfilterandstat", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + }, + { + "name": "log_file", + "type": "txt" + } + ], + "position": { + "left": 4728.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "mpileupfilterandstat", + "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"2\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"10\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"2\\\", \\\"stat_max_depth_min\\\": \\\"100\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.1\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.8\\\"\", \"do_stat\": \"\\\"YES\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}", + "tool_version": "0.08", + "type": "tool", + "user_outputs": [] + }, + "29": { + "annotation": "", + "id": 29, + "input_connections": { + "input_blast_filtered_part1_file": { + "id": 25, + "output_name": "output_file" + }, + "input_blast_filtered_part2_file": { + "id": 26, + "output_name": "output_file" + }, + "input_list_filtered_file": { + "id": 19, + "output_name": "output_file" + }, + "input_mpileup_variant_file": { + "id": 18, + "output_name": "output_file" + }, + "input_read1_part1_trimmed_file": { + "id": 8, + "output_name": "output_read1_file" + }, + "input_read1_part2_trimmed_file": { + "id": 9, + "output_name": "output_read1_file" + }, + "input_read1_row_file": { + "id": 1, + "output_name": "output" + }, + "input_read2_part1_trimmed_file": { + "id": 8, + "output_name": "output_read2_file" + }, + "input_read2_part2_trimmed_file": { + "id": 9, + "output_name": "output_read2_file" + }, + "input_read2_row_file": { + "id": 2, + "output_name": "output" + }, + "input_sam_filtered_part1_file": { + "id": 12, + "output_name": "output_file" + }, + "input_sam_filtered_part2_file": { + "id": 13, + "output_name": "output_file" + }, + "input_sam_row_part1_file": { + "id": 10, + "output_name": "output" + }, + "input_sam_row_part2_file": { + "id": 11, + "output_name": "output" + }, + "input_snp_selected_file": { + "id": 28, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "rapsosnp_stats2x", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 5056.000244140625, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "rapsosnp_stats2x", + "tool_state": "{\"input_blast_filtered_part1_file\": \"null\", \"input_blast_filtered_part2_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"__page__\": 0, \"input_list_filtered_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_read2_row_file\": \"null\", \"input_mpileup_variant_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + } + } +}