Mercurial > repos > peterjc > align_back_trans
diff tools/align_back_trans/align_back_trans.xml @ 0:0c24e4e2177d draft
Uploaded v0.0.3, first stable release.
author | peterjc |
---|---|
date | Thu, 06 Mar 2014 08:58:13 -0500 |
parents | |
children | ec202446408a |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/align_back_trans/align_back_trans.xml Thu Mar 06 08:58:13 2014 -0500 @@ -0,0 +1,131 @@ +<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.3"> + <description>Gives a codon aware alignment</description> + <requirements> + <requirement type="package" version="1.63">biopython</requirement> + <requirement type="python-module">Bio</requirement> + </requirements> + <version_command interpreter="python">align_back_trans.py --version</version_command> + <command interpreter="python"> +align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table" + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." /> + <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> + <option value="1">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate Macronuclear and Dasycladacean</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacterial</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial</option> + <option value="21">21. Trematode Mitochondrial</option> + <option value="22">22. Scenedesmus obliquus</option> + <option value="23">23. Thraustochytrium Mitochondrial</option> + <option value="0">Don't check the translation</option> + </param> + <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> + </inputs> + <outputs> + <data name="out_nuc_align" format="fasta" label="${prot_align.name} (back-translated)"> + <!-- TODO - Replace this with format="input:prot_align" if/when that works --> + <change_format> + <when input_dataset="prot_align" attribute="extension" value="clustal" format="clustal" /> + <when input_dataset="prot_align" attribute="extension" value="phylip" format="phylip" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="prot_align" value="demo_prot_align.fasta" /> + <param name="nuc_file" value="demo_nucs.fasta" /> + <param name="table" value="0" /> + <output name="out_nuc_align" file="demo_nuc_align.fasta" /> + </test> + <test> + <param name="prot_align" value="demo_prot_align.fasta" /> + <param name="nuc_file" value="demo_nucs_trailing_stop.fasta" /> + <param name="table" value="11" /> + <output name="out_nuc_align" file="demo_nuc_align.fasta" /> + </test> + </tests> + <help> +**What it does** + +Takes an input file of aligned protein sequences (typically FASTA or Clustal +format), and a matching file of unaligned nucleotide sequences (FASTA format, +using the same identifiers), and threads the nucleotide sequences onto the +protein alignment to produce a codon aware nucleotide alignment - which can +be viewed as a back translation. + +If you specify one of the standard NCBI genetic codes (recommended), then the +translation is verified. This will allow fuzzy matching if stop codons in the +protein sequence have been reprented as X, and will allow for a trailing stop +codon present in the nucleotide sequences but not the protein. + +Note - the protein and nucleotide sequences must use the same identifers. + +Note - If no translation table is specified, the provided nucleotide sequences +should be exactly three times the length of the protein sequences (exluding the gaps). + +Note - the nucleotide FASTA file may contain extra sequences not in the +protein alignment, they will be ignored. This can be useful if for example +you have a nucleotide FASTA file containing all the genes in an organism, +while the protein alignment is for a specific gene family. + +**Example** + +Given this protein alignment in FASTA format:: + + >Alpha + DEER + >Beta + DE-R + >Gamma + D--R + +and this matching unaligned nucleotide FASTA file:: + + >Alpha + GATGAGGAACGA + >Beta + GATGAGCGU + >Gamma + GATCGG + +the tool would return this nucleotide alignment:: + + >Alpha + GATGAGGAACGA + >Beta + GATGAG---CGU + >Gamma + GAT------CGG + +Notice that all the gaps are multiples of three in length. + + +**Citation** + +This tool uses Biopython, so if you use this Galaxy tool in work leading to a +scientific publication please cite the following paper: + +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. + +This tool is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans + </help> +</tool>