function __construct($argv)
{
parent::__construct($argv, "mgi");
parent::addParameter('files', true, 'all|MGI_Strain|MGI_PhenotypicAllele|MGI_GenePheno|MRK_Sequence|MGI_Geno_Disease|MGI_Geno_NotDisease', 'all', 'all or comma-separated list to process');
parent::addParameter('download_url', false, null, 'ftp://ftp.informatics.jax.org/pub/reports/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "interpro");
parent::addParameter('files', true, 'all', 'all', '');
parent::addParameter('download_url', false, null, 'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', '');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "refseq");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('download_url', false, null, 'ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "ctd");
parent::addParameter('files', true, 'all|chem_gene_ixns|chem_gene_ixn_types|chemicals_diseases|chem_go_enriched|chem_pathways_enriched|genes_diseases|genes_pathways|diseases_pathways|chemicals|diseases|genes|pathways', 'all', 'all or comma-separated list of files to process');
parent::addParameter('download_url', false, null, 'http://ctdbase.org/reports/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "drugbank");
parent::addParameter('files', true, 'all|drugbank', 'all', 'Files to convert');
parent::addParameter('download_url', false, null, 'http://www.drugbank.ca/system/downloads/current/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "orphanet");
parent::addParameter('files', true, 'all|disease|epi|d2s|signs|genes', 'all', 'all or comma-separated list of ontology short names to process');
parent::addParameter('download_url', false, null, 'http://www.orphadata.org/data/xml/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "sabiork");
parent::addParameter('files', true, null, 'all', 'entries to process: comma-separated list or hyphen-separated range');
parent::addParameter('download_url', false, null, 'http://sabiork.h-its.org/sabioRestWebServices/', 'Download API');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "hgnc");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('download_url', false, null, 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/hgnc_complete_set.txt.gz');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "pathwaycommons");
parent::addParameter('files', true, 'all|h**o-sapiens|hprd|humancyc|nci-nature|panther-pathway|phosphositeplus|reactome', 'all', 'biopax OWL files to process');
parent::addParameter('download_url', false, null, 'http://www.pathwaycommons.org/pc2/downloads/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "homologene");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('download_url', false, null, 'ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "gendr");
parent::addParameter('files', true, 'all|gene_manipulations', 'all', 'files to process');
parent::addParameter('download_url', false, null, 'http://genomics.senescence.info/diet/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "pubmed");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('version', false, null, '2013', 'date version of files');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "ipi");
parent::addParameter('files', true, null, 'all|species_xrefs|gene_xrefs|gi2ipi', '', 'files to process');
parent::addParameter('download_url', false, null, 'ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "genage");
parent::addParameter('files', true, 'all|human|models', 'all', 'files to process');
parent::addParameter('download_url', false, null, 'http://genomics.senescence.info/genes/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "biomodels");
// set and print application parameters
parent::addParameter('files', true, null, 'all|curated|biomodel#|start#-end#', 'entries to process: comma-separated list or hyphen-separated range');
parent::addParameter('download_url', false, null, 'http://www.ebi.ac.uk/biomodels/models-main/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "goa");
// parent::addParameter('files',true,'all|arabidopsis|chicken|cow|dicty|dog|fly|human|mouse|pdb|pig|rat|uniprot|worm|yeast|zebrafish','all','all or comma-separated list of files to process');
parent::addParameter('files', true, 'all|arabidopsis|chicken|cow|dicty|dog|fly|human|mouse|pig|rat|worm|yeast|zebrafish', 'all', 'all or comma-separated list of files to process');
parent::addParameter('download_url', false, null, 'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "genbank");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('workspace', false, null, '/data/download/genbank/rsync/', 'directory to place FTP files');
parent::addParameter('download_url', false, null, 'ftp://ftp.ncbi.nih.gov/genbank/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "sider");
// set and print application parameters
parent::addParameter('files', true, 'all|indications|se|freq', 'all', 'all or comma-separated list of ontology short names to process');
parent::addParameter('download_url', false, null, 'http://sideeffects.embl.de/media/download/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "kegg");
parent::addParameter('files', true, 'all|pathway|disease|drug|compound|genome|genes|enzyme|reaction|ko|module|environ|glycan|rpair|rclass', 'all', 'all or comma-separated list of kegg databases');
// brite|
parent::addParameter('download_url', false, null, 'http://rest.kegg.jp/', 'The KEGG REST API');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "affymetrix");
parent::addParameter('files', true, null, 'all', '');
parent::addParameter('version', false, null, '35', 'to set another version to parse from');
parent::addParameter('download_url', false, null, 'http://www.affymetrix.com/support/technical/annotationfilesmain.affx', '');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, 'dbsnp');
// set and print application parameters
parent::addParameter('files', true, null, 'all', 'all|clinical|omim|pharmgkb|snp#,snp#');
parent::addParameter('download_url', false, null, 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&retmode=xml&id=', 'the download url for individual snps');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "mesh");
parent::addParameter('files', true, 'all|descriptors|qualifiers|supplementary', 'all', 'all or comma-separated list of files to process');
parent::addParameter('download_url', false, '', 'ftp://nlmpubs.nlm.nih.gov/online/mesh/.asciimesh/', 'default ftp location');
parent::addParameter('year', false, '', '2014', "Year to process");
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "miriam");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('download_url', false, null, 'http://www.ebi.ac.uk/miriam/main/export/xml/');
parent::addParameter('overwrite', false, 'true|false', 'false', 'overwrite existing files with download option');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "wormbase");
parent::addParameter('files', true, 'all|geneIDs|functional_descriptions|gene_associations|gene_interactions|phenotype_associations', 'all', 'files to process');
parent::addParameter('release', false, null, 'current', 'Release version of WormBase');
parent::addParameter('download_url', false, null, 'ftp://ftp.wormbase.org/pub/wormbase/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "clinicaltrials");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('download_url', false, null, 'http://clinicaltrials.gov/ct2/crawl');
parent::addParameter('overwrite', false, 'true|false', 'false', 'overwrite existing files with download option');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "pubchem");
parent::addParameter('files', true, 'all|compounds|substances|bioassay', 'all', 'files to process');
parent::addParameter('workspace', false, null, '/data/download/pubchem/rsync/', 'directory to mount pubchem FTP server');
parent::addParameter('download_url', false, null, 'ftp://ftp.ncbi.nlm.nih.gov/pubchem/');
parent::initialize();
}
public function __construct($argv)
{
parent::__construct($argv, "iproclass");
parent::addParameter('files', true, 'all', 'all', 'files to process');
parent::addParameter('download', false, 'true|false', 'false', 'set true to download files');
parent::addParameter('download_url', false, null, 'ftp://ftp.pir.georgetown.edu/databases/iproclass/');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, "taxonomy");
parent::addParameter('files', true, 'all|taxdmp', 'taxdmp', 'files to process');
// parent::addParameter('files',true,'all|taxdmp|gi2taxid_nucleotide|gi2taxid_protein','taxdmp','files to process');
parent::addParameter('download', false, 'true|false', 'false');
parent::addParameter('download_url', false, null, 'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip');
parent::initialize();
}
function __construct($argv)
{
parent::__construct($argv, 'omim');
parent::addParameter('files', true, null, 'all|omim#', 'entries to process: comma-separated list or hyphen-separated range');
parent::addParameter('omim_api_url', false, null, 'http://api.omim.org/api/entry?include=all&format=json');
parent::addParameter('omim_api_key', false, null);
parent::addParameter('omim_api_key_file', false, null, 'omim.key', 'A file containing your omim KEY');
parent::initialize();
}
function __construct($argv)
{
//
parent::__construct($argv, "irefindex");
parent::addParameter('files', true, 'all|10090|10116|4932|559292|562|6239|7227|9606', 'all', 'all or comma-separated list of files to process');
parent::addParameter('version', false, '07042015|08122013|03022013|10182011', '07042015', 'dated version of files to download');
parent::addParameter('download_url', false, null, 'http://irefindex.org/download/irefindex/data/current/psi_mitab/MITAB2.6/');
parent::initialize();
}