# HG changeset patch # User sarahinraauzeville # Date 1513686527 18000 # Node ID 512bc1edbfec3a1605c8fd0935efc6c35a9370a4 # Parent 8c5020c490065485444f1a12afa76a9669307f45 Workflow ready to use diff -r 8c5020c49006 -r 512bc1edbfec Galaxy-Workflow-Function_Table_for_Tax4Fun_matrix.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-Function_Table_for_Tax4Fun_matrix.ga Tue Dec 19 07:28:47 2017 -0500 @@ -0,0 +1,275 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Function Table for Tax4Fun matrix", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Abundance file" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 188, + "top": 272 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Abundance file\"}", + "tool_version": null, + "type": "data_input", + "uuid": "9cf27a35-93c1-4040-ab49-2a3290151b18", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Sample file" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 867, + "top": 447 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Sample file\"}", + "tool_version": null, + "type": "data_input", + "uuid": "7a023b93-0768-4247-82a8-29a8d7e3857c", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Tree file" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 868, + "top": 535 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Tree file\"}", + "tool_version": null, + "type": "data_input", + "uuid": "510b6fb7-46f3-44aa-8b04-a0179da33c8d", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "FROGS_biom_to_tsv", + "id": 3, + "input_connections": { + "biom_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FROGS BIOM to TSV", + "outputs": [ + { + "name": "tsv_file", + "type": "tabular" + }, + { + "name": "multi_affi_file", + "type": "tabular" + } + ], + "position": { + "left": 384.5, + "top": 275 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "FROGS_biom_to_tsv", + "tool_state": "{\"extract_multi_align\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"biom_file\": \"null\", \"sequence_file\": \"null\"}", + "tool_version": "2.1.0", + "type": "tool", + "uuid": "64b610df-2ede-492a-ba57-d4f4a70660c0", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "sm_sed_11022014", + "id": 4, + "input_connections": { + "file": { + "id": 3, + "output_name": "tsv_file" + } + }, + "inputs": [], + "label": null, + "name": "Find and replace", + "outputs": [ + { + "name": "outputfile", + "type": "tabular" + } + ], + "position": { + "left": 611.5, + "top": 273.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "sm_sed_11022014", + "tool_state": "{\"__page__\": 0, \"substitut\": \"\\\"\\\"\", \"motif\": \"\\\"Multi-affiliation\\\"\", \"__rerun_remap_job_id__\": null, \"file\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "5985b423-19ac-4ed1-9bba-ccca39acf566", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "FROGS_tsv_to_biom", + "id": 5, + "input_connections": { + "tsv_file": { + "id": 4, + "output_name": "outputfile" + } + }, + "inputs": [], + "label": null, + "name": "FROGS TSV_to_BIOM", + "outputs": [ + { + "name": "biom_file", + "type": "biom1" + }, + { + "name": "sequence_file", + "type": "fasta" + } + ], + "position": { + "left": 835.5, + "top": 277 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "FROGS_tsv_to_biom", + "tool_state": "{\"extract_fasta\": \"\\\"False\\\"\", \"multi_affi_file\": \"null\", \"tsv_file\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "7f82f0f7-7030-49da-a417-c1bcb3e408f2", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "FROGSSTAT_Phyloseq_Import_Data", + "id": 6, + "input_connections": { + "biomfile": { + "id": 5, + "output_name": "biom_file" + }, + "samplefile": { + "id": 1, + "output_name": "output" + }, + "treefile": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FROGSSTAT Phyloseq Import Data", + "outputs": [ + { + "name": "data", + "type": "rdata" + }, + { + "name": "html", + "type": "html" + } + ], + "position": { + "left": 1148, + "top": 282.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "FROGSSTAT_Phyloseq_Import_Data", + "tool_state": "{\"__page__\": 0, \"biomfile\": \"null\", \"samplefile\": \"null\", \"ranks\": \"\\\"Kingdom Phylum Class Order Family Genus Species\\\"\", \"__rerun_remap_job_id__\": null, \"treefile\": \"null\", \"normalization\": \"\\\"False\\\"\"}", + "tool_version": "1.0.1", + "type": "tool", + "uuid": "8bf39361-3272-4b55-aa03-4fb5e7deb6a2", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "smFunctionTable", + "id": 7, + "input_connections": { + "input_matrix": { + "id": 6, + "output_name": "data" + } + }, + "inputs": [], + "label": null, + "name": "Function Table", + "outputs": [ + { + "name": "outputfile_fxn_table", + "type": "txt" + }, + { + "name": "outputfile_fxn_meta", + "type": "txt" + }, + { + "name": "outputfile_method_meta", + "type": "txt" + } + ], + "position": { + "left": 1451.5, + "top": 285.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "smFunctionTable", + "tool_state": "{\"output\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"input_matrix\": \"null\", \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "1d9a3a3b-09af-4c1d-a9b3-53aa80aaa119", + "workflow_outputs": [] + } + }, + "uuid": "1cf5c415-013a-466a-8577-f95d2573f29c" +} \ No newline at end of file