# HG changeset patch # User dereeper # Date 1523885785 14400 # Node ID b9f2901a4b003d811028713228c62006504caff6 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac diff -r 000000000000 -r b9f2901a4b00 Galaxy-Workflow-SNiPlay.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-SNiPlay.ga Mon Apr 16 09:36:25 2018 -0400 @@ -0,0 +1,888 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "SNiPlay Workflow", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 273 + }, + "tool_id": null, + "tool_state": "{}", + "tool_version": null, + "type": "data_input", + "uuid": "6cadf2e0-c934-40e9-b7da-6617917bad24", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 201, + "top": 360 + }, + "tool_id": null, + "tool_state": "{}", + "tool_version": null, + "type": "data_input", + "uuid": "253e89d3-c948-419e-af50-f8c8a448af00", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 201, + "top": 458 + }, + "tool_id": null, + "tool_state": "{}", + "tool_version": null, + "type": "data_input", + "uuid": "c83428cf-c1d4-47a2-98ff-721de1e99d22", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", + "errors": null, + "id": 3, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool VCFtools Filter", + "name": "input" + } + ], + "label": null, + "name": "VCFtools Filter", + "outputs": [ + { + "name": "fileout", + "type": "vcf" + }, + { + "name": "fileout_map", + "type": "tabular" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 411, + "top": 221.81666564941406 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "vcftools_filter_stats_diversity", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"nb_alleles_min\": \"\\\"2\\\"\", \"chromosomes\": \"\\\"\\\"\", \"__page__\": null, \"nb_alleles_max\": \"\\\"4\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"0.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"VCF\\\"\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "631d47f0-20d4-43b2-9201-df377902566b", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/2.0.0", + "errors": null, + "id": 4, + "input_connections": { + "genome": { + "id": 1, + "output_name": "output" + }, + "gff": { + "id": 2, + "output_name": "output" + }, + "vcf": { + "id": 3, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SnpEff", + "name": "gff" + }, + { + "description": "runtime parameter for tool SnpEff", + "name": "genome" + }, + { + "description": "runtime parameter for tool SnpEff", + "name": "vcf" + } + ], + "label": null, + "name": "SnpEff", + "outputs": [ + { + "name": "output", + "type": "vcf" + }, + { + "name": "statsFile", + "type": "html" + }, + { + "name": "log", + "type": "txt" + } + ], + "position": { + "left": 393, + "top": 429 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "snpeff_from_gff_vcf", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"gff\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"genome\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"vcf\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "63658036-2ebe-459c-83d9-a7dd29ff0321", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3.0", + "errors": null, + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "input" + } + ], + "label": null, + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 604, + "top": 326 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "snpsift", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"inverse\": \"\\\"false\\\"\", \"expr\": \"\\\"(FILTER != 'LowQual')\\\"\", \"__rerun_remap_job_id__\": null, \"filtering\": \"{\\\"mode\\\": \\\"entries\\\", \\\"__current_case__\\\": 0}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "4.3.0", + "type": "tool", + "uuid": "1e790f32-adfd-4b0c-bc61-9fc558249a6d", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", + "errors": null, + "id": 6, + "input_connections": { + "input": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool VCFtools Filter", + "name": "input" + } + ], + "label": null, + "name": "VCFtools Filter", + "outputs": [ + { + "name": "fileout", + "type": "vcf" + }, + { + "name": "fileout_map", + "type": "tabular" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 678, + "top": 482.816650390625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "vcftools_filter_stats_diversity", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"nb_alleles_min\": \"\\\"2\\\"\", \"chromosomes\": \"\\\"\\\"\", \"__page__\": null, \"nb_alleles_max\": \"\\\"2\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"0.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"VCF\\\"\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "990bd647-19b2-4286-a1f2-2abe5c2de6fc", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", + "errors": null, + "id": 7, + "input_connections": { + "input": { + "id": 6, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool VCFtools Filter", + "name": "input" + } + ], + "label": null, + "name": "VCFtools Filter", + "outputs": [ + { + "name": "fileout", + "type": "vcf" + }, + { + "name": "fileout_map", + "type": "tabular" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 378, + "top": 716.816650390625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "vcftools_filter_stats_diversity", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"nb_alleles_min\": \"\\\"2\\\"\", \"chromosomes\": \"\\\"\\\"\", \"__page__\": null, \"nb_alleles_max\": \"\\\"2\\\"\", \"type_p\": \"\\\"SNP\\\"\", \"allow_missing\": \"\\\"0.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"plink\\\"\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "12053570-88ed-4d97-8be1-ff9981df4382", + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsstats/2.0.0", + "errors": null, + "id": 8, + "input_connections": { + "filein": { + "id": 6, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool VCFtools Stats", + "name": "filein" + } + ], + "label": null, + "name": "VCFtools Stats", + "outputs": [ + { + "name": "fileout_het", + "type": "txt" + }, + { + "name": "fileout_imiss", + "type": "txt" + }, + { + "name": "fileout_sum", + "type": "txt" + }, + { + "name": "filelog", + "type": "txt" + } + ], + "position": { + "left": 848, + "top": 291.81666564941406 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsstats/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "vcftools_filter_stats_diversity", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"fileout_label\": \"\\\"vcf_stats\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"filein\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "20eed6b5-29e4-4037-b8d8-85b2554c9615", + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsslidingwindow/2.0.0", + "errors": null, + "id": 9, + "input_connections": { + "filein": { + "id": 6, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool VCFtools SlidingWindow", + "name": "group" + }, + { + "description": "runtime parameter for tool VCFtools SlidingWindow", + "name": "filein" + } + ], + "label": null, + "name": "VCFtools SlidingWindow", + "outputs": [ + { + "name": "fileout_snp", + "type": "txt" + }, + { + "name": "fileout_taj", + "type": "txt" + }, + { + "name": "fileout_tstv", + "type": "txt" + }, + { + "name": "fileout_windowed", + "type": "txt" + }, + { + "name": "filelog", + "type": "txt" + }, + { + "name": "fileout_fst", + "type": "txt" + }, + { + "name": "fileout_fst_marker", + "type": "txt" + }, + { + "name": "fileout_windowed_combined", + "type": "txt" + }, + { + "name": "fileout_taj_combined", + "type": "txt" + }, + { + "name": "fileout_tstv_combined", + "type": "txt" + }, + { + "name": "fileout_snp_combined", + "type": "txt" + } + ], + "position": { + "left": 1029, + "top": 242.81666564941406 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsslidingwindow/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "vcftools_filter_stats_diversity", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"group\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"fileout_label\": \"\\\"snp_density\\\"\", \"window\": \"\\\"200000\\\"\", \"filein\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "374c1d03-dbe6-43d8-9a75-b83d5fac56f2", + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snmf/snmf/2.0.0", + "errors": null, + "id": 10, + "input_connections": { + "vcf": { + "id": 6, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool sNMF", + "name": "vcf" + } + ], + "label": null, + "name": "sNMF", + "outputs": [ + { + "name": "best_k_output", + "type": "txt" + }, + { + "name": "best_k_groups", + "type": "txt" + }, + { + "name": "best_k_logfile", + "type": "txt" + }, + { + "name": "outputs", + "type": "txt" + }, + { + "name": "logs", + "type": "txt" + } + ], + "position": { + "left": 1284.800048828125, + "top": 444.1166687011719 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snmf/snmf/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "snmf", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"vcf\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"kmin\": \"\\\"2\\\"\", \"threshold_group\": \"\\\"50\\\"\", \"kmax\": \"\\\"5\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "7dd4c260-bee4-42db-891d-f24fc262e94d", + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_density/2.0.0", + "errors": null, + "id": 11, + "input_connections": { + "filein": { + "id": 6, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SNP density", + "name": "filein" + } + ], + "label": null, + "name": "SNP density", + "outputs": [ + { + "name": "fileout", + "type": "txt" + }, + { + "name": "fileout_bysample", + "type": "txt" + } + ], + "position": { + "left": 1237, + "top": 657.816650390625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_density/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "sniplay", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"fileout_label\": \"\\\"densities\\\"\", \"__page__\": null, \"step\": \"\\\"200000\\\"\", \"__rerun_remap_job_id__\": null, \"filein\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "99a1d523-7782-4c36-ab4f-f09d86212a04", + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_mdsplot/2.0.0", + "errors": null, + "id": 12, + "input_connections": { + "filemap": { + "id": 7, + "output_name": "fileout_map" + }, + "fileped": { + "id": 7, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool MDS plot", + "name": "groups" + }, + { + "description": "runtime parameter for tool MDS plot", + "name": "fileped" + }, + { + "description": "runtime parameter for tool MDS plot", + "name": "filemap" + } + ], + "label": null, + "name": "MDS plot", + "outputs": [ + { + "name": "fileout_matrix", + "type": "txt" + }, + { + "name": "fileout_plot", + "type": "txt" + }, + { + "name": "fileout_log", + "type": "txt" + } + ], + "position": { + "left": 731, + "top": 675.816650390625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_mdsplot/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "sniplay", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"fileped\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"filemap\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"fileout_label\": \"\\\"analyse\\\"\", \"groups\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "16887250-114f-4afb-89c7-9ffd0f0ddec4", + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_pedToFasta/2.0.0", + "errors": null, + "id": 13, + "input_connections": { + "filein": { + "id": 7, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Ped2Fasta", + "name": "filein" + } + ], + "label": null, + "name": "Ped2Fasta", + "outputs": [ + { + "name": "fileout", + "type": "fasta" + } + ], + "position": { + "left": 592, + "top": 907.816650390625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_pedToFasta/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "sniplay", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"fileout_label\": \"\\\"filtered\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"filein\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "e68df48c-2cbe-4f1b-9223-33647b9508b2", + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/ped2bed/2.0.0", + "errors": null, + "id": 14, + "input_connections": { + "map": { + "id": 7, + "output_name": "fileout_map" + }, + "ped": { + "id": 7, + "output_name": "fileout" + } + }, + "inputs": [], + "label": null, + "name": "PLINK: ped2bed", + "outputs": [ + { + "name": "bed", + "type": "txt" + }, + { + "name": "fam", + "type": "txt" + }, + { + "name": "bim", + "type": "txt" + }, + { + "name": "logs", + "type": "txt" + } + ], + "position": { + "left": 934.5, + "top": 714 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/ped2bed/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "sniplay", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"ped\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 36321}]}\", \"map\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 36321}]}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "ffd301d8-d99c-4e4e-9881-f61ad019b4d7", + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/readseq/sniplay_readseq/2.0.0", + "errors": null, + "id": 15, + "input_connections": { + "filein": { + "id": 13, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Readseq", + "name": "filein" + } + ], + "label": null, + "name": "Readseq", + "outputs": [ + { + "name": "fileout_log", + "type": "txt" + }, + { + "name": "fileout", + "type": "txt" + } + ], + "position": { + "left": 835, + "top": 963.816650390625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/readseq/sniplay_readseq/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "readseq", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"fileout_label\": \"\\\"phylip conversion\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"filein\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"format\": \"\\\"12\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "f55fcf51-daac-428f-801f-1b8307bc3d13", + "workflow_outputs": [] + }, + "16": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/fastme/fastme/2.0.0", + "errors": null, + "id": 16, + "input_connections": { + "input": { + "id": 15, + "output_name": "fileout" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool FastME", + "name": "input" + } + ], + "label": null, + "name": "FastME", + "outputs": [ + { + "name": "outputTree", + "type": "nhx" + }, + { + "name": "outputLog", + "type": "txt" + }, + { + "name": "outputBoostrap", + "type": "nhx" + }, + { + "name": "outputMatrix", + "type": "txt" + } + ], + "position": { + "left": 1132, + "top": 925.816650390625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/fastme/fastme/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "fastme", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"distance\": \"\\\"--method=I\\\"\", \"__page__\": null, \"equilibrium\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"bootChoice\": \"{\\\"boot\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"treeRefinement\": \"\\\"--spr\\\"\", \"gammaChoice\": \"{\\\"__current_case__\\\": 1, \\\"gamma\\\": \\\"false\\\"}\", \"fileout_label\": \"\\\"Newick tree\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"typeChoice\": \"{\\\"datatype\\\": \\\"d\\\", \\\"modeldna\\\": \\\"4\\\", \\\"__current_case__\\\": 0}\", \"removeGap\": \"\\\"\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "74189f4d-bd98-46fc-9778-b8e9a698a539", + "workflow_outputs": [] + }, + "17": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_rooting/2.0.0", + "errors": null, + "id": 17, + "input_connections": { + "filein": { + "id": 16, + "output_name": "outputTree" + } + }, + "inputs": [], + "label": null, + "name": "Rooting", + "outputs": [ + { + "name": "fileout_log", + "type": "txt" + }, + { + "name": "fileout", + "type": "nwk,nhx" + } + ], + "position": { + "left": 1296, + "top": 798 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_rooting/2.0.0", + "tool_shed_repository": { + "changeset_revision": null, + "name": "sniplay", + "owner": "dereeper", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"fileout_label\": \"\\\"out tree\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"filein\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 36319}]}\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "ded86308-97bc-4580-adf1-23b1cc86c302", + "workflow_outputs": [] + } + }, + "tags": [], + "uuid": "f3ca58e0-87e5-4314-906e-9d2d34f95dc8" +} diff -r 000000000000 -r b9f2901a4b00 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Apr 16 09:36:25 2018 -0400 @@ -0,0 +1,13 @@ + + + + + + + + + + + + +