Mercurial > repos > peterjc > get_orfs_or_cdss
diff tools/filters/get_orfs_or_cdss.xml @ 0:9cff9a1176ea
Uploaded v0.0.1
| author | peterjc |
|---|---|
| date | Thu, 19 Jan 2012 10:17:10 -0500 |
| parents | |
| children | 922d69bd5258 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/get_orfs_or_cdss.xml Thu Jan 19 10:17:10 2012 -0500 @@ -0,0 +1,147 @@ +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.1"> + <description>e.g. to get peptides from ESTs</description> + <command interpreter="python"> +get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file + </command> + <inputs> + <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> + <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> + <option value="1">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate Macronuclear and Dasycladacean</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacterial</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial</option> + <option value="21">21. Trematode Mitochondrial</option> + <option value="22">22. Scenedesmus obliquus</option> + <option value="23">23. Thraustochytrium Mitochondrial</option> + </param> + <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> + <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> + <option value="CDS">Look for CDSs (with start and stop codons)</option> + </param> + <param name="ends" type="select" value="open" label="Sequence end treatment"> + <option value="open">Open ended (will allow missing start/stop codons at the ends)</option> + <option value="closed">Complete (will check for start/stop codons at the ends)</option> + <!-- TODO? Circular, for using this on finished bacteria etc --> + </param> + + <param name="mode" type="select" label="Selection criteria" help="Suppose a sequence has ORFs/CDSs of lengths 100, 102 and 102 -- which should be taken? These options would return 3, 2 or 1 ORF."> + <option value="all">All ORFs/CDSs from each sequence</option> + <option value="top">All ORFs/CDSs from each sequence with the maximum length</option> + <option value="one">First ORF/CDS from each sequence with the maximum length</option> + </param> + <param name="min_len" type="integer" size="5" value="30" label="Minimum length ORF/CDS (in amino acids, e.g. 30 aa = 90 bp plus any stop codon)"> + </param> + <param name="strand" type="select" label="Strand to search" help="Use the forward only option if your sequence directionality is known (e.g. from poly-A tails, or strand specific RNA sequencing."> + <option value="both">Search both the forward and reverse strand</option> + <option value="forward">Only search the forward strand</option> + <option value="reverse">Only search the reverse strand</option> + </param> + </inputs> + <outputs> + <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" /> + <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" /> + </outputs> + <tests> + <test> + <param name="input_file" value="get_orf_input.fasta" /> + <param name="table" value="1" /> + <param name="ftype" value="CDS" /> + <param name="ends" value="open" /> + <param name="mode" value="all" /> + <param name="min_len" value="10" /> + <param name="strand" value="forward" /> + <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" /> + <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" /> + </test> + <test> + <param name="input_file" value="get_orf_input.fasta" /> + <param name="table" value="11" /> + <param name="ftype" value="CDS" /> + <param name="ends" value="closed" /> + <param name="mode" value="all" /> + <param name="min_len" value="10" /> + <param name="strand" value="forward" /> + <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" /> + <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" /> + </test> + <test> + <param name="input_file" value="get_orf_input.fasta" /> + <param name="table" value="11" /> + <param name="ftype" value="CDS" /> + <param name="ends" value="open" /> + <param name="mode" value="all" /> + <param name="min_len" value="10" /> + <param name="strand" value="forward" /> + <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" /> + <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" /> + </test> + </tests> + <requirements> + <requirement type="python-module">Bio</requirement> + </requirements> + <help> + +**What it does** + +Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ +and Standard Flowgram Format (SFF) are supported), and searches each sequence +for open reading frames (ORFs) or potential coding sequences (CDSs) of the +given minimum length. These are returned as FASTA files of nucleotides and +protein sequences. + +You can choose to have all the ORFs/CDSs above the minimum length for each +sequence (similar to the EMBOSS getorf tool), those with the longest length +equal, or the first ORF/CDS with the longest length (in the special case +where a sequence encodes two or more long ORFs/CDSs of the same length). The +last option is a reasonable choice when the input sequences represent EST or +mRNA sequences, where only one ORF/CDS is expected. + +Note that if no ORFs/CDSs in a sequence match the criteria, there will be no +output for that sequence. + +Also note that the ORFs/CDSs are assigned modified identifiers to distinguish +them from the original full length sequences, by appending a suffix. + +The start and stop codons are taken from the `NCBI Genetic Codes +<http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_. +When searching for ORFs, the sequences will run from stop codon to stop +codon, and any start codons are ignored. When searching for CDSs, the first +potential start codon will be used, giving the longest possible CDS within +each ORF, and thus the longest possible protein sequence. This is useful +for things like BLAST or domain searching, but since this may not be the +correct start codon may not be appropriate for signal peptide detection +etc. + +**Example Usage** + +Given some EST sequences (Sanger capillary reads) assembled into unigenes, +or a transcriptome assembly from some RNA-Seq, each of your nucleotide +sequences should (barring sequencing, assembly errors, frame-shifts etc) +encode one protein as a single ORF/CDS, which you wish to extract (and +perhaps translate into amino acids). + +If your RNS-Seq data was strand specific, and assembled taking this into +account, you should only search for ORFs/CDSs on the forward strand. + +**Citation** + +This tool uses Biopython. If you use this tool in scientific work leading +to a publication, please cite the Biopython application note (and Galaxy +too of course): + +Cock et al 2009. Biopython: freely available Python tools for computational +molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. +http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. + + </help> +</tool>