Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff getdata/get_gb_sp.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getdata/get_gb_sp.xml Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,64 @@ +<tool id="get_gb_sp" name="Get_GB_sp" version="1.0"> + <description> Grab All GenBank Data from a text list of species </description> + <requirements> + <requirement type="perl-module">Bio</requirement> + </requirements> + <command interpreter="perl"> + get_gb_sp.pl $data_file $database $outtype $outfile $nffile 2> error.log + </command> + <inputs> + <param format="txt" name="data_file" type="data" optional="false" label="Text list of species" help="One species per line"/> + + <param name="database" type="select" label="Protein or Nucleotide Data"> + <option value="nucleotide">Nucleotide</option> + <option value="protein">Protein</option> + </param> + + <param name="outtype" type="select" label="Output File Format"> + <option value="fasta">Fasta</option> + <option value="genbank">GenBank</option> + </param> + </inputs> + <outputs> + <data format="txt" name="nffile" label="No genbank data ${tool.name} with ${on_string}" /> + <data format="txt" name="outfile" label="Sequence Data from ${tool.name} with ${on_string}" /> + </outputs> + <help> +**What it does** + +Downloads ALL data from GenBank based on species names. + +------ + +**Inputs** + +A text list of species names (or genus names will retrieve all data for a genus.) + +------ + +**Outputs** + +The user selects which output format to use for data downloaded from GenBank. Options Include:: + 1. GenBank format + 2. FASTA format + +------- + +**Additional Information** + +GenBank format can be converted to phytab or other formats using GenBankstrip. + +Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org + +------- + +**Citations** + +This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following. + +Current Osiris Citation is here + +http://osiris-phylogenetics.blogspot.com/2012/10/citation.html + + </help> +</tool>