Mercurial > repos > cpt > cpt_get_orfs
comparison cpt_get_orfs/get_orfs_or_cdss.xml @ 0:daab1b0e68c1 draft
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author | cpt |
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date | Fri, 13 May 2022 04:52:44 +0000 |
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children | 77da06bc38f5 |
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1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="19.1.0.0"> | |
2 <description>e.g. to get peptides from ESTs</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 <import>cpt-macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"> | |
8 <requirement type="package" version="2019.06.08">regex</requirement> | |
9 </expand> | |
10 <command interpreter="python" detect_errors="aggressive"> | |
11 get_orfs_or_cdss.py $input_file -f $input_file.ext --table $table -t $ftype -e "closed" -m "all" --min_len $min_len --strand $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file --og $out_gff3_file | |
12 </command> | |
13 <inputs> | |
14 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> | |
15 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> | |
16 <option value="1">1. Standard</option> | |
17 <option value="2">2. Vertebrate Mitochondrial</option> | |
18 <option value="3">3. Yeast Mitochondrial</option> | |
19 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | |
20 <option value="5">5. Invertebrate Mitochondrial</option> | |
21 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option> | |
22 <option value="9">9. Echinoderm Mitochondrial</option> | |
23 <option value="10">10. Euplotid Nuclear</option> | |
24 <option value="11">11. Bacterial</option> | |
25 <option value="12">12. Alternative Yeast Nuclear</option> | |
26 <option value="13">13. Ascidian Mitochondrial</option> | |
27 <option value="14">14. Flatworm Mitochondrial</option> | |
28 <option value="15">15. Blepharisma Macronuclear</option> | |
29 <option value="16">16. Chlorophycean Mitochondrial</option> | |
30 <option value="21">21. Trematode Mitochondrial</option> | |
31 <option value="22">22. Scenedesmus obliquus</option> | |
32 <option value="23">23. Thraustochytrium Mitochondrial</option> | |
33 <option value="24">24. Pterobranchia Mitochondrial</option> | |
34 </param> | |
35 <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> | |
36 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> | |
37 <option value="CDS">Look for CDSs (with start and stop codons)</option> | |
38 </param> | |
39 <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)" /> | |
40 <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)."> | |
41 <option value="both">Search both the forward and reverse strand</option> | |
42 <option value="forward">Only search the forward strand</option> | |
43 <option value="reverse">Only search the reverse strand</option> | |
44 </param> | |
45 </inputs> | |
46 <outputs> | |
47 <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" /> | |
48 <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" /> | |
49 <data name="out_bed_file" format="bed6" label="${ftype.value}s (bed)" /> | |
50 <data name="out_gff3_file" format="gff3" label="${ftype.value}s (gff3)" /> | |
51 </outputs> | |
52 <tests> | |
53 <test> | |
54 <param name="input_file" value="Orf_T7In.fasta" /> | |
55 <param name="table" value="11" /> | |
56 <param name="ftype" value="ORF" /> | |
57 <param name="min_len" value="30" /> | |
58 <param name="strand" value="both" /> | |
59 <output name="out_nuc_file" file="Orf_T7Out_Nuc.fasta" /> | |
60 <output name="out_prot_file" file="Orf_T7Out_AA.fasta" /> | |
61 <output name="out_bed_file" file="Orf_T7Out_Bed.bed" /> | |
62 <output name="out_gff3_file" file="Orf_T7Out_Gff.gff3" /> | |
63 </test> | |
64 <test> | |
65 <param name="input_file" value="Orf_In2.fasta" /> | |
66 <param name="table" value="1" /> | |
67 <param name="ftype" value="CDS" /> | |
68 <param name="min_len" value="10" /> | |
69 <param name="strand" value="forward" /> | |
70 <output name="out_nuc_file" file="Orf_Out2T1_Nuc.fasta" /> | |
71 <output name="out_prot_file" file="Orf_Out2T1_AA.fasta" /> | |
72 <output name="out_bed_file" file="Orf_Out2T1_Bed.bed" /> | |
73 <output name="out_gff3_file" file="Orf_Out2T1_Gff.gff3" /> | |
74 </test> | |
75 <test> | |
76 <param name="input_file" value="Orf_In2.fasta" /> | |
77 <param name="table" value="11" /> | |
78 <param name="ftype" value="CDS" /> | |
79 <param name="min_len" value="10" /> | |
80 <param name="strand" value="forward" /> | |
81 <output name="out_nuc_file" file="Orf_Out2T11_Nuc.fasta" /> | |
82 <output name="out_prot_file" file="Orf_Out2T11_AA.fasta" /> | |
83 <output name="out_bed_file" file="Orf_Out2T11_Bed.bed" /> | |
84 <output name="out_gff3_file" file="Orf_Out2T11_Gff.gff3" /> </test> | |
85 </tests> | |
86 <help> | |
87 **What it does** | |
88 | |
89 Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ | |
90 and Standard Flowgram Format (SFF) are supported), and searches each sequence | |
91 for open reading frames (ORFs) or potential coding sequences (CDSs) of the | |
92 given minimum length. These are returned as FASTA files of nucleotides and | |
93 protein sequences. | |
94 | |
95 You can choose to have all the ORFs/CDSs above the minimum length for each | |
96 sequence (similar to the EMBOSS getorf tool), those with the longest length | |
97 equal, or the first ORF/CDS with the longest length (in the special case | |
98 where a sequence encodes two or more long ORFs/CDSs of the same length). The | |
99 last option is a reasonable choice when the input sequences represent EST or | |
100 mRNA sequences, where only one ORF/CDS is expected. | |
101 | |
102 Note that if no ORFs/CDSs in a sequence match the criteria, there will be no | |
103 output for that sequence. | |
104 | |
105 Also note that the ORFs/CDSs are assigned modified identifiers to distinguish | |
106 them from the original full length sequences, by appending a suffix. | |
107 | |
108 The start and stop codons are taken from the `NCBI Genetic Codes | |
109 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_. | |
110 When searching for ORFs, the sequences will run from stop codon to stop | |
111 codon, and any start codons are ignored. When searching for CDSs, the first | |
112 potential start codon will be used, giving the longest possible CDS within | |
113 each ORF, and thus the longest possible protein sequence. This is useful | |
114 for things like BLAST or domain searching, but since this may not be the | |
115 correct start codon, it may not be appropriate for signal peptide detection | |
116 etc. | |
117 | |
118 **Example Usage** | |
119 | |
120 Given some EST sequences (Sanger capillary reads) assembled into unigenes, | |
121 or a transcriptome assembly from some RNA-Seq, each of your nucleotide | |
122 sequences should (barring sequencing, assembly errors, frame-shifts etc) | |
123 encode one protein as a single ORF/CDS, which you wish to extract (and | |
124 perhaps translate into amino acids). | |
125 | |
126 If your RNA-Seq data was strand specific, and assembled taking this into | |
127 account, you should only search for ORFs/CDSs on the forward strand. | |
128 | |
129 **Citation** | |
130 | |
131 If you use this Galaxy tool in work leading to a scientific publication please | |
132 cite the following paper: | |
133 | |
134 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
135 Galaxy tools and workflows for sequence analysis with applications | |
136 in molecular plant pathology. PeerJ 1:e167 | |
137 http://dx.doi.org/10.7717/peerj.167 | |
138 | |
139 This tool uses Biopython, so you may also wish to cite the Biopython | |
140 application note (and Galaxy too of course): | |
141 | |
142 Cock et al (2009). Biopython: freely available Python tools for computational | |
143 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
144 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
145 | |
146 This tool is available to install into other Galaxy Instances via the Galaxy | |
147 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss | |
148 </help> | |
149 <citations> | |
150 <citation type="doi">10.7717/peerj.167</citation> | |
151 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
152 </citations> | |
153 </tool> |