Mercurial > repos > peterjc > get_orfs_or_cdss
comparison tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 5:5208c15805ec draft
Uploaded v0.0.5 dependant on Biopython 1.62
author | peterjc |
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date | Mon, 28 Oct 2013 05:19:38 -0400 |
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children | 705a2e2df7fb |
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1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.5"> | |
2 <description>e.g. to get peptides from ESTs</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.62">biopython</requirement> | |
5 <requirement type="python-module">Bio</requirement> | |
6 </requirements> | |
7 <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> | |
8 <command interpreter="python"> | |
9 get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file | |
10 </command> | |
11 <stdio> | |
12 <!-- Anything other than zero is an error --> | |
13 <exit_code range="1:" /> | |
14 <exit_code range=":-1" /> | |
15 </stdio> | |
16 <inputs> | |
17 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> | |
18 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> | |
19 <option value="1">1. Standard</option> | |
20 <option value="2">2. Vertebrate Mitochondrial</option> | |
21 <option value="3">3. Yeast Mitochondrial</option> | |
22 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | |
23 <option value="5">5. Invertebrate Mitochondrial</option> | |
24 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option> | |
25 <option value="9">9. Echinoderm Mitochondrial</option> | |
26 <option value="10">10. Euplotid Nuclear</option> | |
27 <option value="11">11. Bacterial</option> | |
28 <option value="12">12. Alternative Yeast Nuclear</option> | |
29 <option value="13">13. Ascidian Mitochondrial</option> | |
30 <option value="14">14. Flatworm Mitochondrial</option> | |
31 <option value="15">15. Blepharisma Macronuclear</option> | |
32 <option value="16">16. Chlorophycean Mitochondrial</option> | |
33 <option value="21">21. Trematode Mitochondrial</option> | |
34 <option value="22">22. Scenedesmus obliquus</option> | |
35 <option value="23">23. Thraustochytrium Mitochondrial</option> | |
36 </param> | |
37 <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> | |
38 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> | |
39 <option value="CDS">Look for CDSs (with start and stop codons)</option> | |
40 </param> | |
41 <param name="ends" type="select" value="open" label="Sequence end treatment"> | |
42 <option value="open">Open ended (will allow missing start/stop codons at the ends)</option> | |
43 <option value="closed">Complete (will check for start/stop codons at the ends)</option> | |
44 <!-- TODO? Circular, for using this on finished bacteria etc --> | |
45 </param> | |
46 <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."> | |
47 <option value="all">All ORFs/CDSs from each sequence</option> | |
48 <option value="top">All ORFs/CDSs from each sequence with the maximum length</option> | |
49 <option value="one">First ORF/CDS from each sequence with the maximum length</option> | |
50 </param> | |
51 <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)" /> | |
52 <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."> | |
53 <option value="both">Search both the forward and reverse strand</option> | |
54 <option value="forward">Only search the forward strand</option> | |
55 <option value="reverse">Only search the reverse strand</option> | |
56 </param> | |
57 </inputs> | |
58 <outputs> | |
59 <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" /> | |
60 <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" /> | |
61 </outputs> | |
62 <tests> | |
63 <test> | |
64 <param name="input_file" value="get_orf_input.fasta" /> | |
65 <param name="table" value="1" /> | |
66 <param name="ftype" value="CDS" /> | |
67 <param name="ends" value="open" /> | |
68 <param name="mode" value="all" /> | |
69 <param name="min_len" value="10" /> | |
70 <param name="strand" value="forward" /> | |
71 <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" /> | |
72 <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" /> | |
73 </test> | |
74 <test> | |
75 <param name="input_file" value="get_orf_input.fasta" /> | |
76 <param name="table" value="11" /> | |
77 <param name="ftype" value="CDS" /> | |
78 <param name="ends" value="closed" /> | |
79 <param name="mode" value="all" /> | |
80 <param name="min_len" value="10" /> | |
81 <param name="strand" value="forward" /> | |
82 <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" /> | |
83 <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" /> | |
84 </test> | |
85 <test> | |
86 <param name="input_file" value="get_orf_input.fasta" /> | |
87 <param name="table" value="11" /> | |
88 <param name="ftype" value="CDS" /> | |
89 <param name="ends" value="open" /> | |
90 <param name="mode" value="all" /> | |
91 <param name="min_len" value="10" /> | |
92 <param name="strand" value="forward" /> | |
93 <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" /> | |
94 <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" /> | |
95 </test> | |
96 <test> | |
97 <param name="input_file" value="Ssuis.fasta" /> | |
98 <param name="table" value="11" /> | |
99 <param name="ftype" value="ORF" /> | |
100 <param name="ends" value="open" /> | |
101 <param name="mode" value="all" /> | |
102 <param name="min_len" value="100" /> | |
103 <param name="strand" value="both" /> | |
104 <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" /> | |
105 <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" /> | |
106 </test> | |
107 </tests> | |
108 <help> | |
109 **What it does** | |
110 | |
111 Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ | |
112 and Standard Flowgram Format (SFF) are supported), and searches each sequence | |
113 for open reading frames (ORFs) or potential coding sequences (CDSs) of the | |
114 given minimum length. These are returned as FASTA files of nucleotides and | |
115 protein sequences. | |
116 | |
117 You can choose to have all the ORFs/CDSs above the minimum length for each | |
118 sequence (similar to the EMBOSS getorf tool), those with the longest length | |
119 equal, or the first ORF/CDS with the longest length (in the special case | |
120 where a sequence encodes two or more long ORFs/CDSs of the same length). The | |
121 last option is a reasonable choice when the input sequences represent EST or | |
122 mRNA sequences, where only one ORF/CDS is expected. | |
123 | |
124 Note that if no ORFs/CDSs in a sequence match the criteria, there will be no | |
125 output for that sequence. | |
126 | |
127 Also note that the ORFs/CDSs are assigned modified identifiers to distinguish | |
128 them from the original full length sequences, by appending a suffix. | |
129 | |
130 The start and stop codons are taken from the `NCBI Genetic Codes | |
131 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_. | |
132 When searching for ORFs, the sequences will run from stop codon to stop | |
133 codon, and any start codons are ignored. When searching for CDSs, the first | |
134 potential start codon will be used, giving the longest possible CDS within | |
135 each ORF, and thus the longest possible protein sequence. This is useful | |
136 for things like BLAST or domain searching, but since this may not be the | |
137 correct start codon may not be appropriate for signal peptide detection | |
138 etc. | |
139 | |
140 **Example Usage** | |
141 | |
142 Given some EST sequences (Sanger capillary reads) assembled into unigenes, | |
143 or a transcriptome assembly from some RNA-Seq, each of your nucleotide | |
144 sequences should (barring sequencing, assembly errors, frame-shifts etc) | |
145 encode one protein as a single ORF/CDS, which you wish to extract (and | |
146 perhaps translate into amino acids). | |
147 | |
148 If your RNS-Seq data was strand specific, and assembled taking this into | |
149 account, you should only search for ORFs/CDSs on the forward strand. | |
150 | |
151 **Citation** | |
152 | |
153 If you use this Galaxy tool in work leading to a scientific publication please | |
154 cite the following paper: | |
155 | |
156 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
157 Galaxy tools and workflows for sequence analysis with applications | |
158 in molecular plant pathology. PeerJ 1:e167 | |
159 http://dx.doi.org/10.7717/peerj.167 | |
160 | |
161 This tool uses Biopython, so you may also wish to cite the Biopython | |
162 application note (and Galaxy too of course): | |
163 | |
164 Cock et al (2009). Biopython: freely available Python tools for computational | |
165 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
166 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
167 | |
168 This tool is available to install into other Galaxy Instances via the Galaxy | |
169 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss | |
170 </help> | |
171 </tool> |