# HG changeset patch # User mcharles # Date 1408019320 14400 # Node ID 05949fc8dfe1b05372a4ebf8cb0eeb0c58f77242 # Parent ad321ff1b67da995e577ef6f5936c33c31c0d012 Uploaded diff -r ad321ff1b67d -r 05949fc8dfe1 rapsodyn/Galaxy-Workflow-Rapsodyn_v1.3.ga --- a/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.3.ga Thu Aug 14 08:12:06 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,632 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "Rapsodyn v1.3", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "READ1" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 320, - "top": 201 - }, - "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": 320, - "top": 321 - }, - "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": 320, - "top": 441 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"ASSEMBLY\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "DUBIOUS POSITION" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 320, - "top": 561 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"DUBIOUS POSITION\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "4": { - "annotation": "", - "id": 4, - "input_connections": { - "input_file": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "FASTQ Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 540, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0.4", - "type": "tool", - "user_outputs": [] - }, - "5": { - "annotation": "", - "id": 5, - "input_connections": { - "input_file": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "name": "FASTQ Groomer", - "outputs": [ - { - "name": "output_file", - "type": "fastqsanger" - } - ], - "position": { - "left": 540, - "top": 321 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0.4", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "", - "id": 6, - "input_connections": { - "input_fasta": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "name": "fastaGroomerForMakeBlastdb", - "outputs": [ - { - "name": "output_fasta", - "type": "fasta" - } - ], - "position": { - "left": 540, - "top": 441 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "fastaGroomerForMakeBlastdb", - "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "", - "id": 7, - "input_connections": { - "readtype|input_paired1": { - "id": 4, - "output_name": "output_file" - }, - "readtype|input_paired2": { - "id": 5, - "output_name": "output_file" - } - }, - "inputs": [], - "name": "Sickle", - "outputs": [ - { - "name": "output_single", - "type": "input" - }, - { - "name": "output_paired1", - "type": "fastq" - }, - { - "name": "output_paired2", - "type": "fastq" - }, - { - "name": "output_paired_single", - "type": "fastq" - } - ], - "position": { - "left": 760, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", - "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "8": { - "annotation": "", - "id": 8, - "input_connections": { - "input_file": { - "id": 6, - "output_name": "output_fasta" - } - }, - "inputs": [], - "name": "NCBI BLAST+ makeblastdb", - "outputs": [ - { - "name": "outfile", - "type": "data" - } - ], - "position": { - "left": 760, - "top": 321 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", - "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", - "tool_version": "0.1.00", - "type": "tool", - "user_outputs": [] - }, - "9": { - "annotation": "", - "id": 9, - "input_connections": { - "readtype|input_paired1": { - "id": 7, - "output_name": "output_paired1" - }, - "readtype|input_paired2": { - "id": 7, - "output_name": "output_paired2" - } - }, - "inputs": [], - "name": "Sickle", - "outputs": [ - { - "name": "output_single", - "type": "input" - }, - { - "name": "output_paired1", - "type": "fastq" - }, - { - "name": "output_paired2", - "type": "fastq" - }, - { - "name": "output_paired_single", - "type": "fastq" - } - ], - "position": { - "left": 980, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", - "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "10": { - "annotation": "", - "id": 10, - "input_connections": { - "genomeSource|ownFile": { - "id": 2, - "output_name": "output" - }, - "paired|input1": { - "id": 9, - "output_name": "output_paired1" - }, - "paired|input2": { - "id": 9, - "output_name": "output_paired2" - } - }, - "inputs": [], - "name": "Map with BWA for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - } - ], - "position": { - "left": 1200, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", - "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.2.3", - "type": "tool", - "user_outputs": [] - }, - "11": { - "annotation": "", - "id": 11, - "input_connections": { - "input_sam_file": { - "id": 10, - "output_name": "output" - } - }, - "inputs": [], - "name": "filtersamunique", - "outputs": [ - { - "name": "output_file", - "type": "sam" - } - ], - "position": { - "left": 1420, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "filtersamunique", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - }, - "12": { - "annotation": "", - "id": 12, - "input_connections": { - "input1": { - "id": 11, - "output_name": "output_file" - } - }, - "inputs": [], - "name": "Filter SAM or BAM", - "outputs": [ - { - "name": "output1", - "type": "sam" - } - ], - "position": { - "left": 1640, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1", - "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"yes\\\", \\\"skipBits\\\": null, \\\"__current_case__\\\": 1, \\\"reqBits\\\": \\\"0x0002\\\"}\", \"mapq\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.1.1", - "type": "tool", - "user_outputs": [] - }, - "13": { - "annotation": "", - "id": 13, - "input_connections": { - "source|input1": { - "id": 12, - "output_name": "output1" - }, - "source|ref_file": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "name": "SAM-to-BAM", - "outputs": [ - { - "name": "output1", - "type": "bam" - } - ], - "position": { - "left": 1860, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", - "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", - "tool_version": "1.1.4", - "type": "tool", - "user_outputs": [] - }, - "14": { - "annotation": "", - "id": 14, - "input_connections": { - "reference_source|input_bams_0|input_bam": { - "id": 13, - "output_name": "output1" - }, - "reference_source|ref_file": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "name": "MPileup", - "outputs": [ - { - "name": "output_mpileup", - "type": "pileup" - }, - { - "name": "output_log", - "type": "txt" - } - ], - "position": { - "left": 2080, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", - "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.0.3", - "type": "tool", - "user_outputs": [] - }, - "15": { - "annotation": "", - "id": 15, - "input_connections": { - "input_file": { - "id": 14, - "output_name": "output_mpileup" - } - }, - "inputs": [], - "name": "mpileupfilter", - "outputs": [ - { - "name": "output_file", - "type": "pileup" - } - ], - "position": { - "left": 2300, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "mpileupfilter", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", - "tool_version": "0.05", - "type": "tool", - "user_outputs": [] - }, - "16": { - "annotation": "", - "id": 16, - "input_connections": { - "input_listA": { - "id": 15, - "output_name": "output_file" - }, - "input_listB": { - "id": 3, - "output_name": "output" - } - }, - "inputs": [], - "name": "listfiltering", - "outputs": [ - { - "name": "output_file", - "type": "pileup" - } - ], - "position": { - "left": 2520, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "listfiltering", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - }, - "17": { - "annotation": "", - "id": 17, - "input_connections": { - "input_assembly_file": { - "id": 2, - "output_name": "output" - }, - "input_variant_file": { - "id": 16, - "output_name": "output_file" - } - }, - "inputs": [], - "name": "extractseq", - "outputs": [ - { - "name": "output_file", - "type": "fasta" - } - ], - "position": { - "left": 2740, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "extractseq", - "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.03", - "type": "tool", - "user_outputs": [] - }, - "18": { - "annotation": "", - "id": 18, - "input_connections": { - "db_opts|histdb": { - "id": 8, - "output_name": "outfile" - }, - "query": { - "id": 17, - "output_name": "output_file" - } - }, - "inputs": [], - "name": "NCBI BLAST+ blastn", - "outputs": [ - { - "name": "output1", - "type": "tabular" - } - ], - "position": { - "left": 2960, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", - "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.1.00", - "type": "tool", - "user_outputs": [] - }, - "19": { - "annotation": "", - "id": 19, - "input_connections": { - "input_blastxml_file": { - "id": 18, - "output_name": "output1" - }, - "input_variant_file": { - "id": 16, - "output_name": "output_file" - } - }, - "inputs": [], - "name": "mpileupfilteronblastxml", - "outputs": [ - { - "name": "output_file", - "type": "pileup" - } - ], - "position": { - "left": 3180, - "top": 201 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "mpileupfilteronblastxml", - "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "0.03", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file diff -r ad321ff1b67d -r 05949fc8dfe1 rapsodyn/Galaxy-Workflow-Rapsodyn_v1.31.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.31.ga Thu Aug 14 08:28:40 2014 -0400 @@ -0,0 +1,648 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Rapsodyn v1.31", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "READ1" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 200 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"READ1\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "READ2" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 285 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"READ2\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "ASSEMBLY" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 370 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"ASSEMBLY\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "DUBIOUS POSITION" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 455 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"DUBIOUS POSITION\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "FASTQ Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 428, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", + "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0.4", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "name": "FASTQ Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 428, + "top": 331 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", + "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0.4", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "input_fasta": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "fastaGroomerForMakeBlastdb", + "outputs": [ + { + "name": "output_fasta", + "type": "fasta" + } + ], + "position": { + "left": 428, + "top": 462 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "fastaGroomerForMakeBlastdb", + "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "readtype|input_paired1": { + "id": 4, + "output_name": "output_file" + }, + "readtype|input_paired2": { + "id": 5, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "Sickle", + "outputs": [ + { + "name": "output_single", + "type": "input" + }, + { + "name": "output_combo", + "type": "input" + }, + { + "name": "output_combo_single", + "type": "input" + }, + { + "name": "output_paired1", + "type": "fastq" + }, + { + "name": "output_paired2", + "type": "fastq" + }, + { + "name": "output_paired_single", + "type": "fastq" + } + ], + "position": { + "left": 756, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nikhil-joshi/sickle/sickle/1.33", + "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe_sep\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 2}\", \"trunc_n\": \"\\\"False\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", + "tool_version": "1.33", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "input_file": { + "id": 6, + "output_name": "output_fasta" + } + }, + "inputs": [], + "name": "NCBI BLAST+ makeblastdb", + "outputs": [ + { + "name": "outfile", + "type": "data" + } + ], + "position": { + "left": 756, + "top": 528 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", + "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", + "tool_version": "0.1.00", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "readtype|input_paired1": { + "id": 7, + "output_name": "output_paired1" + }, + "readtype|input_paired2": { + "id": 7, + "output_name": "output_paired2" + } + }, + "inputs": [], + "name": "Sickle", + "outputs": [ + { + "name": "output_single", + "type": "input" + }, + { + "name": "output_combo", + "type": "input" + }, + { + "name": "output_combo_single", + "type": "input" + }, + { + "name": "output_paired1", + "type": "fastq" + }, + { + "name": "output_paired2", + "type": "fastq" + }, + { + "name": "output_paired_single", + "type": "fastq" + } + ], + "position": { + "left": 1084, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nikhil-joshi/sickle/sickle/1.33", + "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe_sep\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 2}\", \"trunc_n\": \"\\\"True\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", + "tool_version": "1.33", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "", + "id": 10, + "input_connections": { + "genomeSource|ownFile": { + "id": 2, + "output_name": "output" + }, + "paired|input1": { + "id": 9, + "output_name": "output_paired1" + }, + "paired|input2": { + "id": 9, + "output_name": "output_paired2" + } + }, + "inputs": [], + "name": "Map with BWA for Illumina", + "outputs": [ + { + "name": "output", + "type": "sam" + } + ], + "position": { + "left": 1412, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", + "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.2.3", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "input_sam_file": { + "id": 10, + "output_name": "output" + } + }, + "inputs": [], + "name": "filtersamunique", + "outputs": [ + { + "name": "output_file", + "type": "sam" + } + ], + "position": { + "left": 1676, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "filtersamunique", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": { + "input1": { + "id": 11, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "Filter SAM or BAM", + "outputs": [ + { + "name": "output1", + "type": "sam" + } + ], + "position": { + "left": 2004, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1", + "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"yes\\\", \\\"skipBits\\\": null, \\\"__current_case__\\\": 1, \\\"reqBits\\\": \\\"0x0002\\\"}\", \"mapq\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.1.1", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "source|input1": { + "id": 12, + "output_name": "output1" + }, + "source|ref_file": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "SAM-to-BAM", + "outputs": [ + { + "name": "output1", + "type": "bam" + } + ], + "position": { + "left": 2332, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", + "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", + "tool_version": "1.1.4", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "", + "id": 14, + "input_connections": { + "reference_source|input_bams_0|input_bam": { + "id": 13, + "output_name": "output1" + }, + "reference_source|ref_file": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "MPileup", + "outputs": [ + { + "name": "output_mpileup", + "type": "pileup" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 2560, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", + "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.0.3", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "", + "id": 15, + "input_connections": { + "input_file": { + "id": 14, + "output_name": "output_mpileup" + } + }, + "inputs": [], + "name": "mpileupfilter", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 2886, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "mpileupfilter", + "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", + "tool_version": "0.05", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "input_listA": { + "id": 15, + "output_name": "output_file" + }, + "input_listB": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "name": "listfiltering", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 3214, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "listfiltering", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "17": { + "annotation": "", + "id": 17, + "input_connections": { + "input_assembly_file": { + "id": 2, + "output_name": "output" + }, + "input_variant_file": { + "id": 16, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "extractseq", + "outputs": [ + { + "name": "output_file", + "type": "fasta" + } + ], + "position": { + "left": 3542, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "extractseq", + "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.03", + "type": "tool", + "user_outputs": [] + }, + "18": { + "annotation": "", + "id": 18, + "input_connections": { + "db_opts|histdb": { + "id": 8, + "output_name": "outfile" + }, + "query": { + "id": 17, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "NCBI BLAST+ blastn", + "outputs": [ + { + "name": "output1", + "type": "tabular" + } + ], + "position": { + "left": 3870, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", + "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.1.00", + "type": "tool", + "user_outputs": [] + }, + "19": { + "annotation": "", + "id": 19, + "input_connections": { + "input_blastxml_file": { + "id": 18, + "output_name": "output1" + }, + "input_variant_file": { + "id": 16, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "mpileupfilteronblastxml", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 4172, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "mpileupfilteronblastxml", + "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "0.03", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file