# HG changeset patch # User gandres # Date 1443020950 14400 # Node ID 66cb91afe9ea2b2281157c6d71bea2e729ec4db5 Uploaded diff -r 000000000000 -r 66cb91afe9ea Galaxy-Workflow-SNiPlay_workflow_final.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-SNiPlay_workflow_final.ga Wed Sep 23 11:09:10 2015 -0400 @@ -0,0 +1,653 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "SNiPlay_workflow_final", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "VCF" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 253.63333129882812, + "top": 239.61666870117188 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"VCF\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Fasta" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 223.63333129882812, + "top": 417.6166687011719 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Fasta\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "GFF" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 306.63330078125, + "top": 580.61669921875 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"GFF\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "genome": { + "id": 1, + "output_name": "output" + }, + "gff": { + "id": 2, + "output_name": "output" + }, + "vcf": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "SnpEff", + "outputs": [ + { + "name": "output", + "type": "vcf" + }, + { + "name": "statsFile", + "type": "html" + }, + { + "name": "log", + "type": "txt" + } + ], + "position": { + "left": 563.63330078125, + "top": 156.61666870117188 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/4.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"gff\": \"null\", \"genome\": \"null\", \"vcf\": \"null\"}", + "tool_version": "4.0", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "input": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "expr" + } + ], + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 863.63330078125, + "top": 334.6166687011719 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.0.0", + "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"expr\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"filtering\": \"{\\\"mode\\\": \\\"entries\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", + "tool_version": "4.0.0", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "filein": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "name": "VCFtools Filter", + "outputs": [ + { + "name": "fileout", + "type": "vcf" + }, + { + "name": "fileout_map", + "type": "txt" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 1164.63330078125, + "top": 300.6166687011719 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1", + "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"None\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"VCF\\\"\", \"filein\": \"null\", \"samples\": \"\\\"None\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", + "tool_version": "1.1.1", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "filein": { + "id": 5, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "VCFtools Filter", + "outputs": [ + { + "name": "fileout", + "type": "vcf" + }, + { + "name": "fileout_map", + "type": "txt" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 1194.433349609375, + "top": 770.88330078125 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1", + "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"plink\\\"\", \"filein\": \"null\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", + "tool_version": "1.1.1", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "filein": { + "id": 5, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "VCFtools Stats", + "outputs": [ + { + "name": "fileout_annot", + "type": "txt" + }, + { + "name": "fileout_het", + "type": "txt" + }, + { + "name": "fileout_imiss", + "type": "txt" + }, + { + "name": "fileout_sum", + "type": "txt" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 1488.683349609375, + "top": 100.10000610351562 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsstats/1.0.0", + "tool_state": "{\"fileout_label\": \"\\\"vcf_stats\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "filein": { + "id": 5, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "VCF tools SlidingWindow", + "outputs": [ + { + "name": "fileout_snp", + "type": "tabular" + }, + { + "name": "fileout_taj", + "type": "tabular" + }, + { + "name": "fileout_tstv", + "type": "tabular" + }, + { + "name": "fileout_windowed", + "type": "tabular" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 1488.683349609375, + "top": 309.1000061035156 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsslidingwindow/1.0.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"window\": \"\\\"200000\\\"\", \"fileout_label\": \"\\\"snp_density\\\"\", \"step\": \"\\\"50000\\\"\", \"filein\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "filein": { + "id": 5, + "output_name": "fileout" + }, + "optional|filefasta": { + "id": 1, + "output_name": "output" + }, + "optional|filegff": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "name": "VCF to Hapmap", + "outputs": [ + { + "name": "fileout", + "type": "txt" + }, + { + "name": "fileout_seq", + "type": "txt" + }, + { + "name": "fileout_fa1", + "type": "fasta" + } + ], + "position": { + "left": 1479.683349609375, + "top": 531.0999755859375 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_vcf2fastaandhapmap/1.1.0", + "tool_state": "{\"fileout_label\": \"\\\"input\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"optional\": \"{\\\"file_opt\\\": \\\"fasta_gff\\\", \\\"filefasta\\\": null, \\\"filegff\\\": null, \\\"__current_case__\\\": 2}\", \"filein\": \"null\"}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "", + "id": 10, + "input_connections": { + "map": { + "id": 6, + "output_name": "fileout_map" + }, + "ped": { + "id": 6, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "plink: ped2bed", + "outputs": [ + { + "name": "bed", + "type": "txt" + }, + { + "name": "fam", + "type": "txt" + }, + { + "name": "bim", + "type": "txt" + }, + { + "name": "logs", + "type": "txt" + } + ], + "position": { + "left": 1488.1666259765625, + "top": 805.5833129882812 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/ped2bed/1.24", + "tool_state": "{\"ped\": \"null\", \"map\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.24", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "filein": { + "id": 6, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "Ped2Fasta", + "outputs": [ + { + "name": "fileout", + "type": "fasta" + } + ], + "position": { + "left": 1491.4833984375, + "top": 1137.4666748046875 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_pedToFasta/1.0.0", + "tool_state": "{\"fileout_label\": \"\\\"filtered\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": { + "filein": { + "id": 9, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "SNP density", + "outputs": [ + { + "name": "fileout", + "type": "tabular" + }, + { + "name": "fileout_bysample", + "type": "tabular" + } + ], + "position": { + "left": 1785.183349609375, + "top": 478.8499755859375 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_density/1.2.0", + "tool_state": "{\"fileout_label\": \"\\\"densities\\\"\", \"__page__\": 0, \"step\": \"\\\"200000\\\"\", \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", + "tool_version": "1.2.0", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "input": { + "id": 9, + "output_name": "fileout_fa1" + } + }, + "inputs": [], + "name": "Diversity by gene", + "outputs": [ + { + "name": "output", + "type": "txt" + }, + { + "name": "log", + "type": "txt" + } + ], + "position": { + "left": 1764.183349609375, + "top": 655.63330078125 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/calculate_diversity/2.1.6", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "2.1.6", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "", + "id": 14, + "input_connections": { + "bed": { + "id": 10, + "output_name": "bed" + }, + "bim": { + "id": 10, + "output_name": "bim" + }, + "fam": { + "id": 10, + "output_name": "fam" + } + }, + "inputs": [], + "name": "Admixture", + "outputs": [ + { + "name": "best_k_output", + "type": "txt" + }, + { + "name": "best_k_logfile", + "type": "txt" + }, + { + "name": "outputs", + "type": "txt" + }, + { + "name": "logs", + "type": "txt" + } + ], + "position": { + "left": 1784.1666259765625, + "top": 839.5833129882812 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/admixture/admixture/1.23", + "tool_state": "{\"__page__\": 0, \"bim\": \"null\", \"__rerun_remap_job_id__\": null, \"kmin\": \"\\\"1\\\"\", \"bed\": \"null\", \"kmax\": \"\\\"5\\\"\", \"fam\": \"null\"}", + "tool_version": "1.23", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "", + "id": 15, + "input_connections": { + "filein": { + "id": 11, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "Readseq", + "outputs": [ + { + "name": "fileout_log", + "type": "txt" + }, + { + "name": "fileout", + "type": "txt" + } + ], + "position": { + "left": 1734, + "top": 1156.75 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/readseq/sniplay_readseq/1.0.2", + "tool_state": "{\"fileout_label\": \"\\\"phylip conversion\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\", \"format\": \"\\\"12\\\"\"}", + "tool_version": "1.0.2", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "input_data": { + "id": 15, + "output_name": "fileout_log" + } + }, + "inputs": [], + "name": "FastME", + "outputs": [ + { + "name": "fileout_log", + "type": "txt" + }, + { + "name": "fileout", + "type": "txt" + } + ], + "position": { + "left": 1969, + "top": 1143.75 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/fastme/sniplay_fastme/1.0.2", + "tool_state": "{\"distance\": \"\\\"I\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"fileout_label\": \"\\\"Newick tree\\\"\", \"input_data\": \"null\", \"model\": \"\\\"4\\\"\"}", + "tool_version": "1.0.2", + "type": "tool", + "user_outputs": [] + }, + "17": { + "annotation": "", + "id": 17, + "input_connections": { + "filein": { + "id": 16, + "output_name": "fileout" + } + }, + "inputs": [], + "name": "Rooting", + "outputs": [ + { + "name": "fileout_log", + "type": "txt" + }, + { + "name": "fileout", + "type": "txt" + } + ], + "position": { + "left": 2224, + "top": 1157.75 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_rooting/1.0.2", + "tool_state": "{\"fileout_label\": \"\\\"out tree\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", + "tool_version": "1.0.2", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file