Mercurial > repos > peterjc > align_back_trans
annotate tools/align_back_trans/align_back_trans.xml @ 6:b27388e5a0bb draft
v0.0.10 removed unused reference to muscle format
author | peterjc |
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date | Mon, 21 Aug 2017 06:26:14 -0400 |
parents | 2c32e8a8990f |
children | 883842b81796 |
rev | line source |
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6 | 1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.10"> |
0 | 2 <description>Gives a codon aware alignment</description> |
3 <requirements> | |
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4 <requirement type="package" version="1.67">biopython</requirement> |
0 | 5 </requirements> |
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6 <version_command> |
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7 python $__tool_directory__/align_back_trans.py --version |
6 | 8 </version_command> |
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9 <command detect_errors="aggressive"> |
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10 python $__tool_directory__/align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table' |
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11 </command> |
0 | 12 <inputs> |
6 | 13 <param name="prot_align" type="data" format="fasta,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." /> |
0 | 14 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> |
15 <option value="1">1. Standard</option> | |
16 <option value="2">2. Vertebrate Mitochondrial</option> | |
17 <option value="3">3. Yeast Mitochondrial</option> | |
18 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | |
19 <option value="5">5. Invertebrate Mitochondrial</option> | |
20 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option> | |
21 <option value="9">9. Echinoderm Mitochondrial</option> | |
22 <option value="10">10. Euplotid Nuclear</option> | |
23 <option value="11">11. Bacterial</option> | |
24 <option value="12">12. Alternative Yeast Nuclear</option> | |
25 <option value="13">13. Ascidian Mitochondrial</option> | |
26 <option value="14">14. Flatworm Mitochondrial</option> | |
27 <option value="15">15. Blepharisma Macronuclear</option> | |
28 <option value="16">16. Chlorophycean Mitochondrial</option> | |
29 <option value="21">21. Trematode Mitochondrial</option> | |
30 <option value="22">22. Scenedesmus obliquus</option> | |
31 <option value="23">23. Thraustochytrium Mitochondrial</option> | |
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32 <option value="24">24. Pterobranchia Mitochondrial</option> |
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33 <option value="25">25. Candidate Division SR1 and Gracilibacteria</option> |
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34 <!-- TODO, these are not in Biopython 1.67 |
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35 <option value="26">26. Pachysolen tannophilus Nuclear</option> |
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36 <option value="26">27. Karyorelict Nuclear</option> |
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37 <option value="26">28. Condylostoma Nuclear</option> |
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38 <option value="26">29. Mesodinium Nuclear</option> |
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39 <option value="26">30. Peritrich Nuclear</option> |
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40 <option value="26">31. Blastocrithidia Nuclear</option> |
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41 --> |
0 | 42 <option value="0">Don't check the translation</option> |
43 </param> | |
44 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> | |
45 </inputs> | |
46 <outputs> | |
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47 <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/> |
0 | 48 </outputs> |
49 <tests> | |
50 <test> | |
51 <param name="prot_align" value="demo_prot_align.fasta" /> | |
52 <param name="nuc_file" value="demo_nucs.fasta" /> | |
53 <param name="table" value="0" /> | |
54 <output name="out_nuc_align" file="demo_nuc_align.fasta" /> | |
55 </test> | |
56 <test> | |
57 <param name="prot_align" value="demo_prot_align.fasta" /> | |
58 <param name="nuc_file" value="demo_nucs_trailing_stop.fasta" /> | |
59 <param name="table" value="11" /> | |
60 <output name="out_nuc_align" file="demo_nuc_align.fasta" /> | |
61 </test> | |
62 </tests> | |
63 <help> | |
64 **What it does** | |
65 | |
66 Takes an input file of aligned protein sequences (typically FASTA or Clustal | |
67 format), and a matching file of unaligned nucleotide sequences (FASTA format, | |
68 using the same identifiers), and threads the nucleotide sequences onto the | |
69 protein alignment to produce a codon aware nucleotide alignment - which can | |
70 be viewed as a back translation. | |
71 | |
72 If you specify one of the standard NCBI genetic codes (recommended), then the | |
73 translation is verified. This will allow fuzzy matching if stop codons in the | |
74 protein sequence have been reprented as X, and will allow for a trailing stop | |
75 codon present in the nucleotide sequences but not the protein. | |
76 | |
77 Note - the protein and nucleotide sequences must use the same identifers. | |
78 | |
79 Note - If no translation table is specified, the provided nucleotide sequences | |
80 should be exactly three times the length of the protein sequences (exluding the gaps). | |
81 | |
82 Note - the nucleotide FASTA file may contain extra sequences not in the | |
83 protein alignment, they will be ignored. This can be useful if for example | |
84 you have a nucleotide FASTA file containing all the genes in an organism, | |
85 while the protein alignment is for a specific gene family. | |
86 | |
87 **Example** | |
88 | |
89 Given this protein alignment in FASTA format:: | |
90 | |
91 >Alpha | |
92 DEER | |
93 >Beta | |
94 DE-R | |
95 >Gamma | |
96 D--R | |
97 | |
98 and this matching unaligned nucleotide FASTA file:: | |
99 | |
100 >Alpha | |
101 GATGAGGAACGA | |
102 >Beta | |
103 GATGAGCGU | |
104 >Gamma | |
105 GATCGG | |
106 | |
107 the tool would return this nucleotide alignment:: | |
108 | |
109 >Alpha | |
110 GATGAGGAACGA | |
111 >Beta | |
112 GATGAG---CGU | |
113 >Gamma | |
114 GAT------CGG | |
115 | |
116 Notice that all the gaps are multiples of three in length. | |
117 | |
118 | |
119 **Citation** | |
120 | |
121 This tool uses Biopython, so if you use this Galaxy tool in work leading to a | |
122 scientific publication please cite the following paper: | |
123 | |
124 Cock et al (2009). Biopython: freely available Python tools for computational | |
125 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
126 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
127 | |
128 This tool is available to install into other Galaxy Instances via the Galaxy | |
129 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans | |
130 </help> | |
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131 <citations> |
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132 <citation type="doi">10.7717/peerj.167</citation> |
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133 <citation type="doi">10.1093/bioinformatics/btp163</citation> |
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134 </citations> |
0 | 135 </tool> |