[ { "name": "Frogs", "docker_name": "Frogs", "description": "16 metabarcoding analysis with Frogs", "version": "0.0.1", "author": "MBB", "options": [ { "name": "results_dir", "type": "output_dir", "value": "\/Results", "label": "Results directory: ", "volumes": [ { "Results": "\/Results" } ] } ], "steps_in": [ { "step_name": "FROGS_2", "tool_name": "FROGS_preprocess", "rule_name": "FROGS_preprocess_PE", "params": [ { "input_name": "read_dir", "origin_command": "raw_read_dir", "origin_name": "read_dir", "origin_step": "input" } ] }, { "step_name": "FROGS_4", "tool_name": "FROGS_cluster", "rule_name": "FROGS_cluster", "params": [ { "input_name": "sequence_file", "origin_command": "FROGS_preprocess_PE", "origin_name": "sequence_file", "origin_step": "FROGS_2" }, { "input_name": "count_file", "origin_command": "FROGS_preprocess_PE", "origin_name": "count_file", "origin_step": "FROGS_2" } ] }, { "step_name": "FROGS", "tool_name": "FROGS_remove_chimera", "rule_name": "FROGS_remove_chimera", "params": [ { "input_name": "sequence_file", "origin_command": "FROGS_cluster", "origin_name": "cluster_seeds", "origin_step": "FROGS_4" }, { "input_name": "abundance_biom", "origin_command": "FROGS_cluster", "origin_name": "abundance_file", "origin_step": "FROGS_4" } ] }, { "step_name": "FROGS_3", "tool_name": "FROGS_filter_OTU", "rule_name": "FROGS_filter_OTU", "params": [ { "input_name": "sequence_file", "origin_command": "FROGS_remove_chimera", "origin_name": "non_chimera_fasta", "origin_step": "FROGS" }, { "input_name": "biom", "origin_command": "FROGS_remove_chimera", "origin_name": "abundance_file", "origin_step": "FROGS" } ] }, { "step_name": "FROGS_5", "tool_name": "FROGS_affiliation", "rule_name": "FROGS_affiliation", "params": [ { "input_name": "fasta", "origin_command": "FROGS_filter_OTU", "origin_name": "filtered_sequences", "origin_step": "FROGS_3" }, { "input_name": "biom", "origin_command": "FROGS_filter_OTU", "origin_name": "abundance_file", "origin_step": "FROGS_3" } ] }, { "step_name": "FROGS_6", "tool_name": "FROGS_filter_affiliation", "rule_name": "FROGS_filter_affiliation", "params": [ { "input_name": "fasta", "origin_command": "FROGS_filter_OTU", "origin_name": "filtered_sequences", "origin_step": "FROGS_3" }, { "input_name": "biom", "origin_command": "FROGS_affiliation", "origin_name": "abundance_file", "origin_step": "FROGS_5" } ] }, { "step_name": "FROGS_8", "tool_name": "FROGS_biom_to_tsv", "rule_name": "FROGS_biom_to_tsv", "params": [ { "input_name": "biom", "origin_command": "FROGS_filter_affiliation", "origin_name": "biom_filtered", "origin_step": "FROGS_6" } ] }, { "step_name": "FROGS_7", "tool_name": "FROGS_phyloseq_stats", "rule_name": "FROGS_phyloseq_stats", "params": [ { "input_name": "biom_file", "origin_command": "FROGS_filter_affiliation", "origin_name": "biom_filtered", "origin_step": "FROGS_6" }, { "input_name": "otu_sequence_file", "origin_command": "FROGS_filter_affiliation", "origin_name": "sequence_file", "origin_step": "FROGS_6" }, { "input_name": "popmap_file", "origin_command": "raw_popmap", "origin_name": "popmap", "origin_step": "input" } ] }, { "step_name": "metabarcoding", "tool_name": "lulu", "rule_name": "lulu", "params": [ { "input_name": "abundance_file", "origin_command": "FROGS_biom_to_tsv", "origin_name": "lulu_abundance_file", "origin_step": "FROGS_8" }, { "input_name": "sequence_file", "origin_command": "FROGS_filter_affiliation", "origin_name": "sequence_file", "origin_step": "FROGS_6" } ] } ], "steps": [ { "title": "FROGS_2", "name": "FROGS_2", "tools": [ "FROGS_preprocess" ], "default": "FROGS_preprocess" }, { "title": "FROGS_4", "name": "FROGS_4", "tools": [ "FROGS_cluster" ], "default": "FROGS_cluster" }, { "title": "FROGS", "name": "FROGS", "tools": [ "FROGS_remove_chimera" ], "default": "FROGS_remove_chimera" }, { "title": "FROGS_3", "name": "FROGS_3", "tools": [ "FROGS_filter_OTU" ], "default": "FROGS_filter_OTU" }, { "title": "FROGS_5", "name": "FROGS_5", "tools": [ "FROGS_affiliation" ], "default": "FROGS_affiliation" }, { "title": "FROGS_6", "name": "FROGS_6", "tools": [ "FROGS_filter_affiliation" ], "default": "FROGS_filter_affiliation" }, { "title": "FROGS_8", "name": "FROGS_8", "tools": [ "FROGS_biom_to_tsv" ], "default": "FROGS_biom_to_tsv" }, { "title": "FROGS_7", "name": "FROGS_7", "tools": [ "FROGS_phyloseq_stats" ], "default": "FROGS_phyloseq_stats" }, { "title": "metabarcoding", "name": "metabarcoding", "tools": [ "lulu" ], "default": "lulu" } ], "input": [ "raw_read_dir", "raw_popmap" ], "params_equals": [], "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/Frogs", "json": { "class": "GraphLinksModel", "linkFromPortIdProperty": "fromPort", "linkToPortIdProperty": "toPort", "modelData": { "position": "-764.5579687500003 -856.0600000000001" }, "nodeDataArray": [ { "name": "FROGS_remove_chimera", "text": "FROGS remove chimera", "size2": "195 110", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "sequence_file", "description": "the sequences in fasta format", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "biom", "value": "abundance_biom", "description": "the abundance file", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "fasta_file", "value": "non_chimera_fasta", "description": "the non chimera sequences", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "biom", "value": "abundance_file", "description": "the abundance file with affiliation", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o3", "type": "html", "value": "summary", "description": "summary", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o4", "type": "link", "value": "linkOut" } ], "description": "Remove PCR chimera in each sample", "version": "3.2.3", "key": "4840997664", "loc": "130 -30" }, { "name": "FROGS_preprocess_PE", "text": "FROGS_preprocess_PE", "size2": "175 110", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "read_dir", "value": "read_dir", "description": "Directory containing the processed radtag reads", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "fasta_file", "value": "sequence_file", "description": "the dereplicated sequences : strictly identical sequence are represented only once", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "tsv", "value": "count_file", "description": "the count of all unique sequences in each sample", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o3", "type": "html", "value": "summary", "description": "summary", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o4", "type": "link", "value": "linkOut" } ], "description": "Merging, Denoising and Dereplication", "version": "3.2.3", "key": "8026992436", "loc": "-370 -30" }, { "name": "FROGS_filter_OTU", "text": "FROGS filter OTU", "size2": "195 135", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "sequence_file", "description": "the sequences in fasta format", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "biom", "value": "biom", "description": "The abundance of each OTU in each sample", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "fasta_file", "value": "filtered_sequences", "description": "The sequences after filtering", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "biom", "value": "abundance_file", "description": "The abundance after filtering", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o3", "type": "tsv", "value": "excluded_file", "description": "The list of the OTUs deleted by filters", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o4", "type": "html", "value": "summary", "description": "The filters and the number of removed sequences", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o5", "type": "link", "value": "linkOut" } ], "description": "Filters OTUs on several criteria", "version": "3.2.3", "key": "8724708950", "loc": "220 -540" }, { "name": "FROGS_cluster", "text": "FROGS cluster", "size2": "155 110", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "sequence_file", "description": "the sequences in fasta format", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "tsv", "value": "count_file", "description": "the count by sample for each sequence", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "fasta_file", "value": "cluster_seeds", "description": "The clusters representative sequences", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "biom", "value": "abundance_file", "description": "The abundance of each cluster in each sample", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o3", "type": "tsv", "value": "cluster_composition", "description": "A text file representing the read composition of each cluster", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o4", "type": "link", "value": "linkOut" } ], "description": "Single-linkage clustering on sequences", "version": "3.2.3", "key": "7214681101", "loc": "-110 -30" }, { "name": "FROGS_affiliation", "text": "FROGS affiliation", "size2": "185 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "fasta", "description": "the sequences in fasta format", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "biom", "value": "biom", "description": "the abundance of each OTU in each sample", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "biom", "value": "abundance_file", "description": "the abundance file with affiliation", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "html", "value": "summary", "description": "summary", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "Adding taxonomic affiliation in abundance file", "version": "3.2.3", "key": "6242321927", "loc": "620 -10" }, { "name": "read_dir", "text": "read_dir", "size2": "", "category": "Data", "strokeWidth": 2, "fill": "#2ecc71", "inservices": [], "outservices": [ { "name": "o1", "type": "read_dir", "value": "raw_read_dir", "description": "", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "unknown", "version": "unknown", "key": -9, "loc": "-600 -60" }, { "name": "FROGS_filter_affiliation", "text": "FROGS filter affiliation", "size2": "220 160", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "fasta", "description": "The sequence file to filter", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "biom", "value": "biom", "description": "The abundance file to filter", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "biom", "value": "biom_filtered", "description": "the abundance file with filtered affiliation", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "fasta_file", "value": "sequence_file", "description": "the filtered sequences", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o3", "type": "tsv", "value": "impacted", "description": "The list of the OTUs deleted or hidden or with updated blast affiliation", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o4", "type": "tsv", "value": "multihit", "description": "The list of blast affiliations for multi-affiliated impacted OTU", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o5", "type": "html", "value": "summary", "description": "summary", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o6", "type": "link", "value": "linkOut" } ], "description": "Filters OTUs on several affiliation criteria", "version": "3.2.3", "key": "3993521995", "loc": "920 -570" }, { "name": "FROGS_phyloseq_stats", "text": "FROGS_phyloseq_stats", "size2": "175 110", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "biom", "value": "biom_file", "description": "The biom file contains the OTU's informations: abundance and taxonomy.", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "fasta_file", "value": "otu_sequence_file", "description": "OTU sequences in fasta format", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i3", "type": "popmap", "value": "popmap_file", "description": "Path to tsv file with metatdata of samples conditions", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "tsv", "value": "alpha_div", "description": "detailed alpha diversity indices in each sample", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "tsv", "value": "wunifrac_div", "description": "wunifrac distance matrix between samples", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "Phyloseq to analyse abundance, diversity and structure", "version": "3.2.3", "key": "6413296569", "loc": "1270 -320" }, { "name": "popmap", "text": "popmap", "size2": "", "category": "Data", "strokeWidth": 2, "fill": "#2ecc71", "inservices": [], "outservices": [ { "name": "o1", "type": "popmap", "value": "raw_popmap", "description": "", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "unknown", "version": "unknown", "key": -10, "loc": "910 -300" }, { "name": "FROGS_biom_to_tsv", "text": "FROGS biom2tsv", "size2": "155 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "biom", "value": "biom", "description": "the abundance of each OTU in each sample", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "tsv", "value": "abundance_file", "description": "output file with the abundance and metadata (tsv)", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "tsv", "value": "lulu_abundance_file", "description": "OTU abundance with samples as columns and OTUs as rows (for lulu)", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "Adding taxonomic affiliation in abundance file", "version": "3.2.3", "key": "2822907117", "loc": "1240 -750" }, { "name": "lulu", "text": "lulu post clustering", "size2": "195 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "tsv", "value": "abundance_file", "description": "OTU table with samples as columns and OTUs as rows, with unique OTU id's as row names", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "fasta_file", "value": "sequence_file", "description": "OTU sequences", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "tsv", "value": "curated_table", "description": "Table of retained OTUs", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "tsv", "value": "otu_map", "description": "Table of information of which daughters were mapped to which parents OTUs", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "A r-package for distribution based post clustering curation of amplicon data.", "version": "latest", "key": "7334609199", "loc": "1370 -560" } ], "linkDataArray": [ { "from": -9, "to": "8026992436", "fromPort": "raw_read_dir", "toPort": "read_dir", "points": [ -541.9458332061768, -58.7, -531.9458332061768, -58.7, -506.7354166507721, -58.7, -506.7354166507721, -28.600000000000005, -481.52500009536743, -28.600000000000005, -471.52500009536743, -28.600000000000005 ] }, { "from": "8026992436", "to": "7214681101", "fromPort": "sequence_file", "toPort": "sequence_file", "points": [ -268.47499990463257, -52.18166608810425, -258.47499990463257, -52.18166608810425, -235, -52.18166608810425, -235, -40.39083304405213, -211.52500009536743, -40.39083304405213, -201.52500009536743, -40.39083304405213 ] }, { "from": "8026992436", "to": "7214681101", "fromPort": "count_file", "toPort": "count_file", "points": [ -268.47499990463257, -28.600000000000005, -258.47499990463257, -28.600000000000005, -235, -28.600000000000005, -235, -16.809166955947877, -211.52500009536743, -16.809166955947877, -201.52500009536743, -16.809166955947877 ] }, { "from": "7214681101", "to": "4840997664", "fromPort": "cluster_seeds", "toPort": "sequence_file", "points": [ -18.47499990463257, -52.18166608810425, -8.474999904632568, -52.18166608810425, 0, -52.18166608810425, 0, -40.39083304405213, 8.474999904632568, -40.39083304405213, 18.47499990463257, -40.39083304405213 ] }, { "from": "7214681101", "to": "4840997664", "fromPort": "abundance_file", "toPort": "abundance_biom", "points": [ -18.47499990463257, -28.600000000000005, -8.474999904632568, -28.600000000000005, 0, -28.600000000000005, 0, -16.809166955947877, 8.474999904632568, -16.809166955947877, 18.47499990463257, -16.809166955947877 ] }, { "from": "4840997664", "to": "8724708950", "fromPort": "non_chimera_fasta", "toPort": "sequence_file", "points": [ 240.64453125, -51.677832031250006, 250.64453125, -51.677832031250006, 250.64453125, -278.75, 99.35546875, -278.75, 99.35546875, -551.388916015625, 109.35546875, -551.388916015625 ] }, { "from": "4840997664", "to": "8724708950", "fromPort": "abundance_file", "toPort": "biom", "points": [ 240.64453125, -28.6, 250.64453125, -28.6, 250.64453125, -278.75, 99.35546875, -278.75, 99.35546875, -528.311083984375, 109.35546875, -528.311083984375 ] }, { "from": "8724708950", "to": "6242321927", "fromPort": "filtered_sequences", "toPort": "fasta", "points": [ 330.64453125, -571.6204427083334, 340.64453125, -571.6204427083334, 340, -571.6204427083334, 340, -571.6204427083334, 540, -571.6204427083334, 540, -212, 508, -212, 508, -18.888916015625, 504.35546875, -18.888916015625, 514.35546875, -18.888916015625 ] }, { "from": "8724708950", "to": "6242321927", "fromPort": "abundance_file", "toPort": "biom", "points": [ 330.64453125, -551.3889160156251, 340.64453125, -551.3889160156251, 340, -551.3889160156251, 340, -551.3889160156251, 540, -551.3889160156251, 540, -212, 508, -212, 508, 4.188916015624999, 504.35546875, 4.188916015624999, 514.35546875, 4.188916015624999 ] }, { "from": "6242321927", "to": "3993521995", "fromPort": "abundance_file", "toPort": "biom", "points": [ 725.64453125, -18.888916015625, 735.64453125, -18.888916015625, 761.25, -18.888916015625, 761.25, -559.561083984375, 786.85546875, -559.561083984375, 796.85546875, -559.561083984375 ] }, { "from": "8724708950", "to": "3993521995", "fromPort": "filtered_sequences", "toPort": "fasta", "points": [ 330.64453125, -577.3130533854168, 340.64453125, -577.3130533854168, 563.75, -577.3130533854168, 563.75, -582.638916015625, 786.85546875, -582.638916015625, 796.85546875, -582.638916015625 ] }, { "from": "3993521995", "to": "6413296569", "fromPort": "sequence_file", "toPort": "otu_sequence_file", "points": [ 1043.14453125, -591.3315266927084, 1053.14453125, -591.3315266927084, 1106.25, -591.3315266927084, 1106.25, -318.6, 1159.35546875, -318.6, 1169.35546875, -318.6 ] }, { "from": "3993521995", "to": "6413296569", "fromPort": "biom_filtered", "toPort": "biom_file", "points": [ 1043.14453125, -614.4093587239583, 1053.14453125, -614.4093587239583, 1106.25, -614.4093587239583, 1106.25, -341.67783203125, 1159.35546875, -341.67783203125, 1169.35546875, -341.67783203125 ] }, { "from": -10, "to": "6413296569", "fromPort": "raw_popmap", "toPort": "popmap_file", "points": [ 967.614990234375, -298.70000000000005, 977.614990234375, -298.70000000000005, 1068.4852294921875, -298.70000000000005, 1068.4852294921875, -295.52216796874995, 1159.35546875, -295.52216796874995, 1169.35546875, -295.52216796874995 ] }, { "from": "3993521995", "to": "2822907117", "fromPort": "biom_filtered", "toPort": "biom", "points": [ 1043.14453125, -620.1019694010417, 1053.14453125, -620.1019694010417, 1096.25, -620.1019694010417, 1096.25, -747.35, 1139.35546875, -747.35, 1149.35546875, -747.35 ] }, { "from": "2822907117", "fromPort": "abundance_file", "toPort": "", "points": [ 1308.26123046875, -758.888916015625, 1298.26123046875, -758.888916015625, 1274.8391716586266, -758.888916015625, 1274.8391716586266, -721.3550391139429, 1251.4171128485032, -721.3550391139429, 1241.4171128485032, -721.3550391139429 ] }, { "from": "2822907117", "to": "7334609199", "fromPort": "lulu_abundance_file", "toPort": "abundance_file", "points": [ 1330.64453125, -735.811083984375, 1340.64453125, -735.811083984375, 1340.64453125, -655, 1249.35546875, -655, 1249.35546875, -568.888916015625, 1259.35546875, -568.888916015625 ] }, { "from": "3993521995", "to": "7334609199", "fromPort": "sequence_file", "toPort": "sequence_file", "points": [ 1043.14453125, -597.0241373697918, 1061.14453125, -597.0241373697918, 1155.25, -597.0241373697918, 1155.25, -545.811083984375, 1249.35546875, -545.811083984375, 1259.35546875, -545.811083984375 ] } ], "version": 2 }, "yaml": "{\nname: \"Frogs\",\ndocker_name: \"Frogs\",\ndescription: \"16 metabarcoding analysis with Frogs\",\nversion: \"0.0.1\",\nauthor: \"MBB\",\noptions: [\n {\n name: \"results_dir\",\n type: \"output_dir\",\n value: \"\/Results\",\n label: \"Results directory: \",\n volumes: [Results: \"\/Results\"]\n },\n],\nsteps_in: [\n{ step_name: \"FROGS_2\", tool_name: \"FROGS_preprocess\", rule_name: \"FROGS_preprocess_PE\",\n params: [\n { input_name: read_dir, origin_command: raw_read_dir, origin_name: read_dir, origin_step: input},\n ]\n},\n{ step_name: \"FROGS_4\", tool_name: \"FROGS_cluster\", rule_name: \"FROGS_cluster\",\n params: [\n { input_name: sequence_file, origin_command: FROGS_preprocess_PE, origin_name: sequence_file, origin_step: FROGS_2},\n { input_name: count_file, origin_command: FROGS_preprocess_PE, origin_name: count_file, origin_step: FROGS_2},\n ]\n},\n{ step_name: \"FROGS\", tool_name: \"FROGS_remove_chimera\", rule_name: \"FROGS_remove_chimera\",\n params: [\n { input_name: sequence_file, origin_command: FROGS_cluster, origin_name: cluster_seeds, origin_step: FROGS_4},\n { input_name: abundance_biom, origin_command: FROGS_cluster, origin_name: abundance_file, origin_step: FROGS_4},\n ]\n},\n{ step_name: \"FROGS_3\", tool_name: \"FROGS_filter_OTU\", rule_name: \"FROGS_filter_OTU\",\n params: [\n { input_name: sequence_file, origin_command: FROGS_remove_chimera, origin_name: non_chimera_fasta, origin_step: FROGS},\n { input_name: biom, origin_command: FROGS_remove_chimera, origin_name: abundance_file, origin_step: FROGS},\n ]\n},\n{ step_name: \"FROGS_5\", tool_name: \"FROGS_affiliation\", rule_name: \"FROGS_affiliation\",\n params: [\n { input_name: fasta, origin_command: FROGS_filter_OTU, origin_name: filtered_sequences, origin_step: FROGS_3},\n { input_name: biom, origin_command: FROGS_filter_OTU, origin_name: abundance_file, origin_step: FROGS_3},\n ]\n},\n{ step_name: \"FROGS_6\", tool_name: \"FROGS_filter_affiliation\", rule_name: \"FROGS_filter_affiliation\",\n params: [\n { input_name: fasta, origin_command: FROGS_filter_OTU, origin_name: filtered_sequences, origin_step: FROGS_3},\n { input_name: biom, origin_command: FROGS_affiliation, origin_name: abundance_file, origin_step: FROGS_5},\n ]\n},\n{ step_name: \"FROGS_8\", tool_name: \"FROGS_biom_to_tsv\", rule_name: \"FROGS_biom_to_tsv\",\n params: [\n { input_name: biom, origin_command: FROGS_filter_affiliation, origin_name: biom_filtered, origin_step: FROGS_6},\n ]\n},\n{ step_name: \"FROGS_7\", tool_name: \"FROGS_phyloseq_stats\", rule_name: \"FROGS_phyloseq_stats\",\n params: [\n { input_name: biom_file, origin_command: FROGS_filter_affiliation, origin_name: biom_filtered, origin_step: FROGS_6},\n { input_name: otu_sequence_file, origin_command: FROGS_filter_affiliation, origin_name: sequence_file, origin_step: FROGS_6},\n { input_name: popmap_file, origin_command: raw_popmap, origin_name: popmap, origin_step: input},\n ]\n},\n{ step_name: \"metabarcoding\", tool_name: \"lulu\", rule_name: \"lulu\",\n params: [\n { input_name: abundance_file, origin_command: FROGS_biom_to_tsv, origin_name: lulu_abundance_file, origin_step: FROGS_8},\n { input_name: sequence_file, origin_command: FROGS_filter_affiliation, origin_name: sequence_file, origin_step: FROGS_6},\n ]\n},\n],\nsteps: [\n { title: \"FROGS_2\", name: \"FROGS_2\", tools: [FROGS_preprocess], default: \"FROGS_preprocess\" },\n { title: \"FROGS_4\", name: \"FROGS_4\", tools: [FROGS_cluster], default: \"FROGS_cluster\" },\n { title: \"FROGS\", name: \"FROGS\", tools: [FROGS_remove_chimera], default: \"FROGS_remove_chimera\" },\n { title: \"FROGS_3\", name: \"FROGS_3\", tools: [FROGS_filter_OTU], default: \"FROGS_filter_OTU\" },\n { title: \"FROGS_5\", name: \"FROGS_5\", tools: [FROGS_affiliation], default: \"FROGS_affiliation\" },\n { title: \"FROGS_6\", name: \"FROGS_6\", tools: [FROGS_filter_affiliation], default: \"FROGS_filter_affiliation\" },\n { title: \"FROGS_8\", name: \"FROGS_8\", tools: [FROGS_biom_to_tsv], default: \"FROGS_biom_to_tsv\" },\n { title: \"FROGS_7\", name: \"FROGS_7\", tools: [FROGS_phyloseq_stats], default: \"FROGS_phyloseq_stats\" },\n { title: \"metabarcoding\", name: \"metabarcoding\", tools: [lulu], default: \"lulu\" },\n],\ninput: [\"raw_read_dir\",\"raw_popmap\",],\nparams_equals: [\n\n]\n}\n" } ]