[ { "id": "FROGS_affiliation_customDB", "name": "FROGS affiliation customDB", "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_customDB", "command": "taxonomic_affiliation.py", "category": "FROGS", "output_dir": "FROGS_affiliation_customDB", "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" }, { "name": "FROGS_fasta_db", "type": "fasta_file", "description": "fasta file with sames seqID as FROGS_tax_db" }, { "name": "FROGS_tax_db", "type": "taxonomyDB", "description": "tabulate file : 'SeqID\tKingdom;Phylum;Class;Order;Family;Genus;Species'. All taxonomies need to be define with the exact same number of rank separate by ';'. Set 'unclassified' for unknown rank" } ], "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_customDB_threads", "prefix": "-p", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "FROGS_affiliation_customDB_rdp", "prefix": "--rdp", "type": "checkbox", "value": false, "label": "Also perform RDP assignation ?" } ] } ], "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_affiliation_customDB,\n name: FROGS affiliation customDB,\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_customDB,\n command: \"taxonomic_affiliation.py\",\n category: \"FROGS\",\n output_dir: FROGS_affiliation_customDB,\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 { name: FROGS_fasta_db, type: \"fasta_file\", description: \"fasta file with sames seqID as FROGS_tax_db\"},\n { name: FROGS_tax_db, type: \"taxonomyDB\", description: \"tabulate file : 'SeqID\\tKingdom;Phylum;Class;Order;Family;Genus;Species'. All taxonomies need to be define with the exact same number of rank separate by ';'. Set 'unclassified' for unknown rank\"}\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_customDB_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_customDB_rdp,\n prefix: --rdp,\n type: checkbox,\n value: False,\n label: \"Also perform RDP assignation ?\",\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\/v3.2.3.tar.gz\",\n # \"tar -zxvf v3.2.3.tar.gz\",\n # \"cd FROGS-3.2.3\",\n # \"mkdir bin\",\n # \"export PYTHONPATH=$PYTHONPATH:\/opt\/biotools\/FROGS-3.2.3\/lib\",\n # ],\n # scipy: [\n # \"apt-get install python3-scipy\" # demande confirmation\n # ],\n # ncbi-blast-2.10.1: [\n # \"cd \/opt\/biotools\/\",\n # \"wget ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.10.1\/ncbi-blast-2.10.1+-x64-linux.tar.gz\",\n # \"tar xvzf ncbi-blast-2.10.1+-x64-linux.tar.gz\",\n # ],\n # Needleall 6.6.0.0: [\n # # requires pdf and png support\n # \"apt-get install -y libhpdf-dev libpng-dev\",\n # \"cd \/opt\/biotools\/\",\n # \"wget ftp:\/\/emboss.open-bio.org\/pub\/EMBOSS\/EMBOSS-6.6.0.tar.gz\",\n # \"tar xvf EMBOSS-6.6.0.tar.gz\",\n # \"cd EMBOSS-6.6.0\",\n # \".\/configure --prefix=\/opt\/biotools\/EMBOSS-6.6.0\",\n # \"make\",\n # \"make install\",\n # ],\n # ant : [\"apt-get install ant\"],\n # RDPclasifier: [\n # \"\/opt\/biotools\/conda\/bin\/conda install -y -c bioconda rdptools\",\n # \"rdp=$(ls \/opt\/biotools\/conda\/share\/rdptools*\/classifier.jar)\",\n # \"chmod a+x $rdp\",\n # \"classify=$(echo $rdp |sed 's\/\\\/classifier.jar$\/\/')\",\n # \"export PATH=$PATH:$classify\",\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-3.2.3\/libexec\/.\",\n # # add RDP to FROGS\n # \"ln -s opt\/biotools\/RDPTools\/classifier.jar \/opt\/biotools\/FROGS-3.2.3\/libexec\/.\",\n\n # # add needleall to FROGS\n # \"ln -s \/opt\/biotools\/EMBOSS-6.6.0\/emboss\/needleall \/opt\/biotools\/FROGS-3.2.3\/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" } ]