[ { "id": "FROGS_preprocess", "name": "FROGS preprocess", "article": "10.1093\/bib\/bbab318", "website": "http:\/\/frogs.toulouse.inrae.fr\/", "git": "https:\/\/github.com\/geraldinepascal\/FROGS", "description": "Merging, Denoising and Dereplication", "version": "4.1.0", "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html", "multiqc": "custom", "commands": [ { "name": "FROGS_preprocess_SE", "cname": "FROGS_preprocess_SE", "command": "preprocess.py", "category": "FROGS", "output_dir": "FROGS_preprocess_SE", "inputs": [ { "name": "read_dir", "type": "SE_read_dir", "description": "Directory containing the processed reads" } ], "outputs": [ { "name": "sequence_file", "file": "dereplicated.fasta", "type": "fasta_file", "description": "the dereplicated sequences : strictly identical sequence are represented only once" }, { "name": "count_file", "file": "count.tsv", "type": "tsv", "description": "the count of all unique sequences in each sample" }, { "name": "summary", "file": "report.html", "type": "html", "description": "summary" } ], "options": [ { "name": "FROGS_preprocess_threads", "prefix": "-p", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "FROGS_preprocess_sequencing_protocol", "prefix": "", "type": "radio", "choices": [ { "standard": "illumina standard" }, { "without_primers": "without_primers" } ], "value": "without_primers", "label": "FROGS guidelines for clustering" }, { "name": "FROGS_preprocess_min_amplicon_size", "prefix": "", "type": "numeric", "value": 10, "min": 0, "max": "NA", "step": 1, "label": "The minimum size for the amplicons (with primers)" }, { "name": "FROGS_preprocess_max_amplicon_size", "prefix": "", "type": "numeric", "value": 10000, "min": 0, "max": "NA", "step": 1, "label": "The maximum size for the amplicons (with primers)" }, { "name": "FROGS_preprocess_five_prim_primer", "prefix": "", "type": "text", "value": "", "label": "The 5' primer sequence" }, { "name": "FROGS_preprocess_three_prim_primer", "prefix": "", "type": "text", "value": "", "label": "The 3' primer sequence" } ] }, { "name": "FROGS_preprocess_PE", "cname": "FROGS_preprocess_PE", "command": "preprocess.py", "category": "FROGS", "output_dir": "FROGS_preprocess_PE", "inputs": [ { "name": "read_dir", "type": "PE_read_dir", "description": "Directory containing the processed reads" } ], "outputs": [ { "name": "sequence_file", "file": "dereplicated.fasta", "type": "fasta_file", "description": "the dereplicated sequences : strictly identical sequence are represented only once" }, { "name": "count_file", "file": "count.tsv", "type": "tsv", "description": "the count of all unique sequences in each sample" }, { "name": "summary", "file": "report.html", "type": "html", "description": "summary" } ], "options": [ { "name": "FROGS_preprocess_threads", "prefix": "-p", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "FROGS_preprocess_sequencing_protocol", "prefix": "", "type": "radio", "choices": [ { "standard": "illumina standard" }, { "without_primers": "without_primers" } ], "value": "without_primers", "label": "FROGS guidelines for clustering" }, { "name": "FROGS_preprocess_min_amplicon_size", "prefix": "", "type": "numeric", "value": 10, "min": 0, "max": "NA", "step": 1, "label": "The minimum size for the amplicons (with primers)" }, { "name": "FROGS_preprocess_max_amplicon_size", "prefix": "", "type": "numeric", "value": 10000, "min": 0, "max": "NA", "step": 1, "label": "The maximum size for the amplicons (with primers)" }, { "name": "FROGS_preprocess_PE_R1_size", "prefix": "", "type": "numeric", "value": 300, "min": 20, "max": "NA", "step": 1, "label": "The maximum read1 size" }, { "name": "FROGS_preprocess_PE_R2_size", "prefix": "", "type": "numeric", "value": 300, "min": 20, "max": "NA", "step": 1, "label": "The maximum read2 size" }, { "name": "FROGS_preprocess_five_prim_primer", "prefix": "", "type": "text", "value": "", "label": "The 5' primer sequence" }, { "name": "FROGS_preprocess_three_prim_primer", "prefix": "", "type": "text", "value": "", "label": "The 3' primer sequence" } ] } ], "install": [], "citations": { "frogs": [ " Maria Bernard, Olivier Ru\u00e9, Mahendra Mariadassou and G\u00e9raldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093\/bib\/bbab318 " ] }, "yaml": "{\n id: FROGS_preprocess,\n name: FROGS preprocess,\n article: 10.1093\/bib\/bbab318,\n website: \"http:\/\/frogs.toulouse.inrae.fr\/\",\n git: \"https:\/\/github.com\/geraldinepascal\/FROGS\",\n description: \"Merging, Denoising and Dereplication\",\n version: \"4.1.0\",\n documentation: \"http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: FROGS_preprocess_SE,\n cname: FROGS_preprocess_SE,\n command: \"preprocess.py\",\n category: \"FROGS\",\n output_dir: FROGS_preprocess_SE,\n inputs: \n [\n { name: \"read_dir\", type: \"SE_read_dir\", description: \"Directory containing the processed reads\" },\n ],\n outputs:\n [\n { name: \"sequence_file\", file: \"dereplicated.fasta\", type: \"fasta_file\", description: \"the dereplicated sequences : strictly identical sequence are represented only once\"},\n { name: \"count_file\", file: \"count.tsv\", type: \"tsv\", description: \"the count of all unique sequences in each sample\"},\n { name: \"summary\", file: \"report.html\", type: \"html\", description: \"summary\"}\n ],\n options:\n [\n {\n name: FROGS_preprocess_threads,\n prefix: -p,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: FROGS_preprocess_sequencing_protocol,\n prefix: \"\",\n type: \"radio\",\n choices:\n [\n standard: \"illumina standard\",\n without_primers: \"without_primers\",\n ],\n value: \"without_primers\",\n label: \"FROGS guidelines for clustering\",\n },\n {\n name: FROGS_preprocess_min_amplicon_size,\n prefix: \"\",\n type: numeric,\n value: 10,\n min: 0,\n max: NA,\n step: 1,\n label: \"The minimum size for the amplicons (with primers)\",\n },\n {\n name: FROGS_preprocess_max_amplicon_size,\n prefix: \"\",\n type: numeric,\n value: 10000,\n min: 0,\n max: NA,\n step: 1,\n label: \"The maximum size for the amplicons (with primers)\",\n },\n {\n name: FROGS_preprocess_five_prim_primer,\n prefix: \"\",\n type: \"text\",\n value: \"\",\n label: \"The 5' primer sequence\",\n },\n {\n name: FROGS_preprocess_three_prim_primer,\n prefix: \"\",\n type: \"text\",\n value: \"\",\n label: \"The 3' primer sequence\",\n },\n ],\n },\n {\n name: FROGS_preprocess_PE,\n cname: FROGS_preprocess_PE,\n command: \"preprocess.py\",\n category: \"FROGS\",\n output_dir: FROGS_preprocess_PE,\n inputs: \n [\n { name: \"read_dir\", type: \"PE_read_dir\", description: \"Directory containing the processed reads\" },\n ],\n outputs:\n [\n { name: \"sequence_file\", file: \"dereplicated.fasta\", type: \"fasta_file\", description: \"the dereplicated sequences : strictly identical sequence are represented only once\"},\n { name: \"count_file\", file: \"count.tsv\", type: \"tsv\", description: \"the count of all unique sequences in each sample\"},\n { name: \"summary\", file: \"report.html\", type: \"html\", description: \"summary\"}\n ],\n options:\n [\n {\n name: FROGS_preprocess_threads,\n prefix: -p,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: FROGS_preprocess_sequencing_protocol,\n prefix: \"\",\n type: \"radio\",\n choices:\n [\n standard: \"illumina standard\",\n without_primers: \"without_primers\",\n ],\n value: \"without_primers\",\n label: \"FROGS guidelines for clustering\",\n },\n {\n name: FROGS_preprocess_min_amplicon_size,\n prefix: \"\",\n type: numeric,\n value: 10,\n min: 0,\n max: NA,\n step: 1,\n label: \"The minimum size for the amplicons (with primers)\",\n },\n {\n name: FROGS_preprocess_max_amplicon_size,\n prefix: \"\",\n type: numeric,\n value: 10000,\n min: 0,\n max: NA,\n step: 1,\n label: \"The maximum size for the amplicons (with primers)\",\n },\n {\n name: FROGS_preprocess_PE_R1_size,\n prefix: \"\",\n type: numeric,\n value: 300,\n min: 20,\n max: NA,\n step: 1,\n label: \"The maximum read1 size\",\n },\n {\n name: FROGS_preprocess_PE_R2_size,\n prefix: \"\",\n type: numeric,\n value: 300,\n min: 20,\n max: NA,\n step: 1,\n label: \"The maximum read2 size\",\n },\n # {\n # name: FROGS_preprocess_PE_mismatch_rate,\n # prefix: \"\",\n # type: numeric,\n # value: 100,\n # min: 20,\n # max: NA,\n # step: 1,\n # label: \"The maximum rate of mismatch in the overlap region\",\n # },\n {\n name: FROGS_preprocess_five_prim_primer,\n prefix: \"\",\n type: \"text\",\n value: \"\",\n label: \"The 5' primer sequence\",\n },\n {\n name: FROGS_preprocess_three_prim_primer,\n prefix: \"\",\n type: \"text\",\n value: \"\",\n label: \"The 3' primer sequence\",\n },\n ],\n },\n ],\n install:\n {\n # perl: [\n # \"sudo apt-get install python3 perl\" # deja install\u00e9\n # ],\n # frogs: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/geraldinepascal\/FROGS\/archive\/v4.1.0.tar.gz\",\n # \"tar -zxvf v4.1.0.tar.gz\",\n # \"cd FROGS-4.1.0\",\n # \"mkdir bin\"\n # ],\n # scipy: [\n # \"apt-get install python3-scipy\" # demande confirmation\n # ],\n # vsearch 2.17.0: [\n # \"apt-get install autoconf libz-dev libbz2-dev\", # deja install\u00e9\n # \"cd \/opt\/biotools\/\",\n # \"wget https:\/\/github.com\/torognes\/vsearch\/archive\/v2.17.0.tar.gz\",\n # \"tar xzf v2.17.0.tar.gz\",\n # \"cd vsearch-2.17.0\",\n # \".\/autogen.sh\",\n # \".\/configure\",\n # \"make\",\n # \"make install\"\n # ],\n # cutadapt 4.0: [\n # \"pip3 install cutadapt==4.0\",\n # ],\n },\n citations: {\n frogs: [\n \" Maria Bernard, Olivier Ru\u00e9, Mahendra Mariadassou and G\u00e9raldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093\/bib\/bbab318 \"\n ]\n }\n}\n" } ]