[ { "id": "FROGS_affiliation", "name": "FROGS affiliation", "article": "10.1093\/bib\/bbab318", "website": "http:\/\/frogs.toulouse.inrae.fr\/", "git": "https:\/\/github.com\/geraldinepascal\/FROGS", "description": "Adding taxonomic affiliation in abundance file", "version": "4.1.0", "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html", "multiqc": "generic_iframe", "commands": [ { "name": "FROGS_affiliation", "command": "taxonomic_affiliation.py", "category": "FROGS", "output_dir": "FROGS_affiliation", "inputs": [ { "name": "fasta", "type": "fasta_file", "description": "the sequences in fasta format" }, { "name": "biom", "type": "biom", "description": "the abundance of each OTU in each sample" } ], "outputs": [ { "name": "abundance_file", "file": "tax_affiliation.biom", "type": "biom", "description": "the abundance file with affiliation" }, { "name": "summary", "file": "affi_report.html", "type": "html", "description": "summary" } ], "options": [ { "name": "FROGS_affiliation_threads", "prefix": "-p", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "FROGS_affiliation_rdp", "prefix": "--rdp", "type": "checkbox", "value": false, "label": "Also perform RDP assignation ?" }, { "name": "FROGS_affiliation_reference_fasta", "type": "select", "choices": [ { "BOLD_COI-5P": "\/FROGS_taxonomy\/COI\/BOLD_COI-5P" }, { "MIDORI": "\/FROGS_taxonomy\/COI\/MIDORI" }, { "COInr": "\/FROGS_taxonomy\/COInr" }, { "DAIRYdb": "\/FROGS_taxonomy\/DAIRYdb" }, { "Diat.barcode": "\/FROGS_taxonomy\/Diat.barcode" }, { "EZBioCloud": "\/FROGS_taxonomy\/EZBioCloud" }, { "MaarjAM": "\/FROGS_taxonomy\/MaarjAM" }, { "MiDas": "\/FROGS_taxonomy\/MiDas" }, { "PHYMYCO_DB": "\/FROGS_taxonomy\/PHYMYCO_DB" }, { "PR2": "\/FROGS_taxonomy\/PR2" }, { "rbcL": "\/FROGS_taxonomy\/rbcL" }, { "rpoB": "\/FROGS_taxonomy\/rpoB" }, { "silva_138.1_16S": "\/FROGS_taxonomy\/SILVA\/16S" }, { "silva_138.1_18S": "\/FROGS_taxonomy\/SILVA\/18S" }, { "silva_138.1_23S": "\/FROGS_taxonomy\/SILVA\/23S" }, { "silva_138.1_28S": "\/FROGS_taxonomy\/SILVA\/28S " }, { "silva_138.1_LSU": "\/FROGS_taxonomy\/SILVA\/LSU" }, { "silva_138.1_SSU": "\/FROGS_taxonomy\/SILVA\/SSU" }, { "Unite": "\/FROGS_taxonomy\/Unite" }, { "gyrB": "\/FROGS_taxonomy\/gyrB" }, { "microgreendb": "\/FROGS_taxonomy\/microgreendb" } ], "value": "\/FROGS_taxonomy\/SILVA\/16S", "label": "Taxonomy source" } ] } ], "install": [], "data": [ { "name": "FROGS_taxonomy", "type": "directory" } ], "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_affiliation,\n name: FROGS affiliation,\n article: 10.1093\/bib\/bbab318,\n website: \"http:\/\/frogs.toulouse.inrae.fr\/\",\n git: \"https:\/\/github.com\/geraldinepascal\/FROGS\",\n description: \"Adding taxonomic affiliation in abundance file\",\n version: \"4.1.0\",\n documentation: \"http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html\",\n multiqc: \"generic_iframe\",\n commands:\n [\n {\n name: FROGS_affiliation,\n command: \"taxonomic_affiliation.py\",\n category: \"FROGS\",\n output_dir: FROGS_affiliation,\n inputs: \n [\n { name: fasta, type: \"fasta_file\", description: \"the sequences in fasta format\"},\n { name: biom, type: \"biom\", description: \"the abundance of each OTU in each sample\"}\n ],\n outputs:\n [\n { name: \"abundance_file\", file: \"tax_affiliation.biom\", type: \"biom\", description: \"the abundance file with affiliation\"},\n { name: \"summary\", file: \"affi_report.html\", type: \"html\", description: \"summary\"}\n ],\n options:\n [\n {\n name: FROGS_affiliation_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_affiliation_rdp,\n prefix: --rdp,\n type: checkbox,\n value: False,\n label: \"Also perform RDP assignation ?\",\n },\n {\n name: FROGS_affiliation_reference_fasta,\n type: select,\n choices: [\n BOLD_COI-5P: \"\/FROGS_taxonomy\/COI\/BOLD_COI-5P\",\n MIDORI: \"\/FROGS_taxonomy\/COI\/MIDORI\",\n COInr: \"\/FROGS_taxonomy\/COInr\",\n DAIRYdb: \"\/FROGS_taxonomy\/DAIRYdb\",\n Diat.barcode: \"\/FROGS_taxonomy\/Diat.barcode\",\n EZBioCloud: \"\/FROGS_taxonomy\/EZBioCloud\",\n MaarjAM: \"\/FROGS_taxonomy\/MaarjAM\",\n MiDas: \"\/FROGS_taxonomy\/MiDas\",\n PHYMYCO_DB: \"\/FROGS_taxonomy\/PHYMYCO_DB\",\n PR2: \"\/FROGS_taxonomy\/PR2\",\n rbcL: \"\/FROGS_taxonomy\/rbcL\",\n rpoB: \"\/FROGS_taxonomy\/rpoB\",\n silva_138.1_16S: \"\/FROGS_taxonomy\/SILVA\/16S\",\n silva_138.1_18S: \"\/FROGS_taxonomy\/SILVA\/18S\",\n silva_138.1_23S: \"\/FROGS_taxonomy\/SILVA\/23S\",\n silva_138.1_28S: \"\/FROGS_taxonomy\/SILVA\/28S \",\n silva_138.1_LSU: \"\/FROGS_taxonomy\/SILVA\/LSU\",\n silva_138.1_SSU: \"\/FROGS_taxonomy\/SILVA\/SSU\",\n Unite: \"\/FROGS_taxonomy\/Unite\",\n gyrB: \"\/FROGS_taxonomy\/gyrB\",\n microgreendb: \"\/FROGS_taxonomy\/microgreendb\",\n ],\n value: \"\/FROGS_taxonomy\/SILVA\/16S\",\n label: \"Taxonomy source\"\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 # ncbi-blast-2.10.1: [\n # \"cd \/opt\/biotools\/\",\n # \"wget ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.10.1\/ncbi-blast-2.10.1+-x64-linux.tar.gz\",\n # \"tar xvzf ncbi-blast-2.10.1+-x64-linux.tar.gz\",\n # ],\n # Needleall 6.6.0.0: [\n # # requires pdf and png support\n # \"apt-get install -y libhpdf-dev libpng-dev\", \n # \"cd \/opt\/biotools\/\",\n # \"wget ftp:\/\/emboss.open-bio.org\/pub\/EMBOSS\/EMBOSS-6.6.0.tar.gz\",\n # \"tar xvf EMBOSS-6.6.0.tar.gz\",\n # \"cd EMBOSS-6.6.0\",\n # \".\/configure --prefix=\/opt\/biotools\/EMBOSS-6.6.0\",\n # \"make\",\n # \"make install\", \n # ],\n # ant : [\"apt-get install ant\"],\n # RDPclasifier: [\n # \"cd \/opt\/biotools\/\",\n # \"git clone https:\/\/github.com\/rdpstaff\/RDPTools.git\",\n # \"cd RDPTools\",\n # \"git checkout 2.0.3\",\n # \"git submodule init\",\n # \"git submodule update\",\n # \"make\",\n # ],\n # frogs_post_install: [\n # # add blast to FROGS\n # \"ln -s \/opt\/biotools\/ncbi-blast-2.10.1+\/bin\/blastn \/opt\/biotools\/FROGS-4.1.0\/libexec\/.\",\n # # add RDP to FROGS\n # \"ln -s opt\/biotools\/RDPTools\/classifier.jar \/opt\/biotools\/FROGS-4.1.0\/libexec\/.\",\n \n # # add needleall to FROGS\n # \"ln -s \/opt\/biotools\/EMBOSS-6.6.0\/emboss\/needleall \/opt\/biotools\/FROGS-4.1.0\/libexec\/.\"\n\n # ],\n },\n data: [\n {\n name: FROGS_taxonomy,\n type: directory\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" } ]