Mercurial > repos > gandres > sniplay_workflow
changeset 2:142784232700 draft default tip
Deleted selected files
author | gandres |
---|---|
date | Wed, 14 Oct 2015 05:32:19 -0400 (2015-10-14) |
parents | 6c3581822cad |
children | |
files | Galaxy-Workflow-SNiPlay_workflow_final.ga |
diffstat | 1 files changed, 0 insertions(+), 653 deletions(-) [+] |
line wrap: on
line diff
--- a/Galaxy-Workflow-SNiPlay_workflow_final.ga Wed Oct 14 05:31:37 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,653 +0,0 @@ -{ - "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