Mercurial > repos > peterjc > get_orfs_or_cdss
annotate tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 11:d51db443aaa4 draft
v0.2.3 Python 3 compatible print function.
author | peterjc |
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date | Wed, 30 May 2018 08:33:20 -0400 |
parents | 01b0488d9cfb |
children | 71905a6d52a7 |
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11 | 1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.3"> |
5 | 2 <description>e.g. to get peptides from ESTs</description> |
3 <requirements> | |
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4 <requirement type="package" version="1.67">biopython</requirement> |
5 | 5 </requirements> |
10 | 6 <version_command> |
7 python $__tool_directory__/get_orfs_or_cdss.py --version | |
8 </version_command> | |
9 <command detect_errors="aggressive"> | |
10 python $__tool_directory__/get_orfs_or_cdss.py | |
11 -i '$input_file' | |
12 -f '$input_file.ext' | |
13 --table '$table' | |
14 -t '$ftype' | |
15 -e '$ends' | |
16 -m '$mode' | |
17 --min_len '$min_len' | |
18 -s '$strand' | |
19 --on '$out_nuc_file' | |
20 --op '$out_prot_file' | |
21 --ob '$out_bed_file' | |
22 --og '$out_gff3_file' | |
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23 </command> |
5 | 24 <inputs> |
25 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> | |
26 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> | |
27 <option value="1">1. Standard</option> | |
28 <option value="2">2. Vertebrate Mitochondrial</option> | |
29 <option value="3">3. Yeast Mitochondrial</option> | |
30 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | |
31 <option value="5">5. Invertebrate Mitochondrial</option> | |
32 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option> | |
33 <option value="9">9. Echinoderm Mitochondrial</option> | |
34 <option value="10">10. Euplotid Nuclear</option> | |
35 <option value="11">11. Bacterial</option> | |
36 <option value="12">12. Alternative Yeast Nuclear</option> | |
37 <option value="13">13. Ascidian Mitochondrial</option> | |
38 <option value="14">14. Flatworm Mitochondrial</option> | |
39 <option value="15">15. Blepharisma Macronuclear</option> | |
40 <option value="16">16. Chlorophycean Mitochondrial</option> | |
41 <option value="21">21. Trematode Mitochondrial</option> | |
42 <option value="22">22. Scenedesmus obliquus</option> | |
43 <option value="23">23. Thraustochytrium Mitochondrial</option> | |
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44 <option value="24">24. Pterobranchia Mitochondrial</option> |
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45 <option value="25">25. Candidate Division SR1 and Gracilibacteria</option> |
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46 <!-- TODO, these are not in Biopython 1.67 |
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47 <option value="26">26. Pachysolen tannophilus Nuclear</option> |
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48 <option value="26">27. Karyorelict Nuclear</option> |
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49 <option value="26">28. Condylostoma Nuclear</option> |
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50 <option value="26">29. Mesodinium Nuclear</option> |
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51 <option value="26">30. Peritrich Nuclear</option> |
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52 <option value="26">31. Blastocrithidia Nuclear</option> |
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53 --> |
5 | 54 </param> |
11 | 55 <param name="ftype" type="select" value="true" label="Look for ORFs or CDSs"> |
5 | 56 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> |
57 <option value="CDS">Look for CDSs (with start and stop codons)</option> | |
58 </param> | |
59 <param name="ends" type="select" value="open" label="Sequence end treatment"> | |
60 <option value="open">Open ended (will allow missing start/stop codons at the ends)</option> | |
61 <option value="closed">Complete (will check for start/stop codons at the ends)</option> | |
62 <!-- TODO? Circular, for using this on finished bacteria etc --> | |
63 </param> | |
64 <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."> | |
65 <option value="all">All ORFs/CDSs from each sequence</option> | |
66 <option value="top">All ORFs/CDSs from each sequence with the maximum length</option> | |
67 <option value="one">First ORF/CDS from each sequence with the maximum length</option> | |
68 </param> | |
69 <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)" /> | |
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70 <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)."> |
5 | 71 <option value="both">Search both the forward and reverse strand</option> |
72 <option value="forward">Only search the forward strand</option> | |
73 <option value="reverse">Only search the reverse strand</option> | |
74 </param> | |
75 </inputs> | |
76 <outputs> | |
77 <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" /> | |
78 <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" /> | |
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79 <data name="out_bed_file" format="bed6" label="${ftype.value}s (bed)" /> |
8 | 80 <data name="out_gff3_file" format="gff3" label="${ftype.value}s (gff3)" /> |
5 | 81 </outputs> |
82 <tests> | |
83 <test> | |
84 <param name="input_file" value="get_orf_input.fasta" /> | |
85 <param name="table" value="1" /> | |
86 <param name="ftype" value="CDS" /> | |
87 <param name="ends" value="open" /> | |
88 <param name="mode" value="all" /> | |
89 <param name="min_len" value="10" /> | |
90 <param name="strand" value="forward" /> | |
91 <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" /> | |
92 <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" /> | |
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93 <output name="out_bed_file" file="get_orf_input.t1_bed_out.bed" /> |
8 | 94 <output name="out_gff3_file" file="get_orf_input.t1_gff3_out.gff3" /> |
5 | 95 </test> |
96 <test> | |
97 <param name="input_file" value="get_orf_input.fasta" /> | |
98 <param name="table" value="11" /> | |
99 <param name="ftype" value="CDS" /> | |
100 <param name="ends" value="closed" /> | |
101 <param name="mode" value="all" /> | |
102 <param name="min_len" value="10" /> | |
103 <param name="strand" value="forward" /> | |
104 <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" /> | |
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105 <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" /> |
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106 <output name="out_bed_file" file="get_orf_input.t11_bed_out.bed" /> |
8 | 107 <output name="out_gff3_file" file="get_orf_input.t11_gff3_out.gff3" /> |
5 | 108 </test> |
109 <test> | |
110 <param name="input_file" value="get_orf_input.fasta" /> | |
111 <param name="table" value="11" /> | |
112 <param name="ftype" value="CDS" /> | |
113 <param name="ends" value="open" /> | |
114 <param name="mode" value="all" /> | |
115 <param name="min_len" value="10" /> | |
116 <param name="strand" value="forward" /> | |
117 <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" /> | |
118 <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" /> | |
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119 <output name="out_bed_file" file="get_orf_input.t11_open_bed_out.bed" /> |
8 | 120 <output name="out_gff3_file" file="get_orf_input.t11_open_gff3_out.gff3" /> |
5 | 121 </test> |
122 <test> | |
123 <param name="input_file" value="Ssuis.fasta" /> | |
124 <param name="table" value="11" /> | |
125 <param name="ftype" value="ORF" /> | |
126 <param name="ends" value="open" /> | |
127 <param name="mode" value="all" /> | |
128 <param name="min_len" value="100" /> | |
129 <param name="strand" value="both" /> | |
130 <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" /> | |
131 <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" /> | |
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132 <output name="out_bed_file" file="get_orf_input.Suis_ORF.bed" /> |
8 | 133 <output name="out_gff3_file" file="get_orf_input.Suis_ORF.gff3" /> |
5 | 134 </test> |
135 </tests> | |
136 <help> | |
137 **What it does** | |
138 | |
139 Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ | |
140 and Standard Flowgram Format (SFF) are supported), and searches each sequence | |
141 for open reading frames (ORFs) or potential coding sequences (CDSs) of the | |
142 given minimum length. These are returned as FASTA files of nucleotides and | |
143 protein sequences. | |
144 | |
145 You can choose to have all the ORFs/CDSs above the minimum length for each | |
146 sequence (similar to the EMBOSS getorf tool), those with the longest length | |
147 equal, or the first ORF/CDS with the longest length (in the special case | |
148 where a sequence encodes two or more long ORFs/CDSs of the same length). The | |
149 last option is a reasonable choice when the input sequences represent EST or | |
150 mRNA sequences, where only one ORF/CDS is expected. | |
151 | |
152 Note that if no ORFs/CDSs in a sequence match the criteria, there will be no | |
153 output for that sequence. | |
154 | |
155 Also note that the ORFs/CDSs are assigned modified identifiers to distinguish | |
156 them from the original full length sequences, by appending a suffix. | |
157 | |
158 The start and stop codons are taken from the `NCBI Genetic Codes | |
159 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_. | |
160 When searching for ORFs, the sequences will run from stop codon to stop | |
161 codon, and any start codons are ignored. When searching for CDSs, the first | |
162 potential start codon will be used, giving the longest possible CDS within | |
163 each ORF, and thus the longest possible protein sequence. This is useful | |
164 for things like BLAST or domain searching, but since this may not be the | |
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165 correct start codon, it may not be appropriate for signal peptide detection |
5 | 166 etc. |
167 | |
168 **Example Usage** | |
169 | |
170 Given some EST sequences (Sanger capillary reads) assembled into unigenes, | |
171 or a transcriptome assembly from some RNA-Seq, each of your nucleotide | |
172 sequences should (barring sequencing, assembly errors, frame-shifts etc) | |
173 encode one protein as a single ORF/CDS, which you wish to extract (and | |
174 perhaps translate into amino acids). | |
175 | |
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176 If your RNA-Seq data was strand specific, and assembled taking this into |
5 | 177 account, you should only search for ORFs/CDSs on the forward strand. |
178 | |
179 **Citation** | |
180 | |
181 If you use this Galaxy tool in work leading to a scientific publication please | |
182 cite the following paper: | |
183 | |
184 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
185 Galaxy tools and workflows for sequence analysis with applications | |
186 in molecular plant pathology. PeerJ 1:e167 | |
187 http://dx.doi.org/10.7717/peerj.167 | |
188 | |
189 This tool uses Biopython, so you may also wish to cite the Biopython | |
190 application note (and Galaxy too of course): | |
191 | |
192 Cock et al (2009). Biopython: freely available Python tools for computational | |
193 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
194 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
195 | |
196 This tool is available to install into other Galaxy Instances via the Galaxy | |
197 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss | |
198 </help> | |
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199 <citations> |
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200 <citation type="doi">10.7717/peerj.167</citation> |
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201 <citation type="doi">10.1093/bioinformatics/btp163</citation> |
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202 </citations> |
5 | 203 </tool> |