Mercurial > repos > peterjc > get_orfs_or_cdss
annotate tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 9:a06ad07431ba draft
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
author | peterjc |
---|---|
date | Wed, 10 May 2017 13:24:46 -0400 |
parents | 09a8be9247ca |
children | 01b0488d9cfb |
rev | line source |
---|---|
9
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.1"> |
5 | 2 <description>e.g. to get peptides from ESTs</description> |
3 <requirements> | |
9
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
4 <requirement type="package" version="1.67">biopython</requirement> |
5 | 5 </requirements> |
6 <stdio> | |
7 <!-- Anything other than zero is an error --> | |
8 <exit_code range="1:" /> | |
9 <exit_code range=":-1" /> | |
10 </stdio> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
11 <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> |
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
12 <command interpreter="python"> |
8 | 13 get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file --og $out_gff3_file |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
14 </command> |
5 | 15 <inputs> |
16 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> | |
17 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> | |
18 <option value="1">1. Standard</option> | |
19 <option value="2">2. Vertebrate Mitochondrial</option> | |
20 <option value="3">3. Yeast Mitochondrial</option> | |
21 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | |
22 <option value="5">5. Invertebrate Mitochondrial</option> | |
23 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option> | |
24 <option value="9">9. Echinoderm Mitochondrial</option> | |
25 <option value="10">10. Euplotid Nuclear</option> | |
26 <option value="11">11. Bacterial</option> | |
27 <option value="12">12. Alternative Yeast Nuclear</option> | |
28 <option value="13">13. Ascidian Mitochondrial</option> | |
29 <option value="14">14. Flatworm Mitochondrial</option> | |
30 <option value="15">15. Blepharisma Macronuclear</option> | |
31 <option value="16">16. Chlorophycean Mitochondrial</option> | |
32 <option value="21">21. Trematode Mitochondrial</option> | |
33 <option value="22">22. Scenedesmus obliquus</option> | |
34 <option value="23">23. Thraustochytrium Mitochondrial</option> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
35 <option value="24">24. Pterobranchia Mitochondrial</option> |
9
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
36 <option value="25">25. Candidate Division SR1 and Gracilibacteria</option> |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
37 <!-- TODO, these are not in Biopython 1.67 |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
38 <option value="26">26. Pachysolen tannophilus Nuclear</option> |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
39 <option value="26">27. Karyorelict Nuclear</option> |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
40 <option value="26">28. Condylostoma Nuclear</option> |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
41 <option value="26">29. Mesodinium Nuclear</option> |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
42 <option value="26">30. Peritrich Nuclear</option> |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
43 <option value="26">31. Blastocrithidia Nuclear</option> |
a06ad07431ba
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
peterjc
parents:
8
diff
changeset
|
44 --> |
5 | 45 </param> |
46 <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> | |
47 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> | |
48 <option value="CDS">Look for CDSs (with start and stop codons)</option> | |
49 </param> | |
50 <param name="ends" type="select" value="open" label="Sequence end treatment"> | |
51 <option value="open">Open ended (will allow missing start/stop codons at the ends)</option> | |
52 <option value="closed">Complete (will check for start/stop codons at the ends)</option> | |
53 <!-- TODO? Circular, for using this on finished bacteria etc --> | |
54 </param> | |
55 <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."> | |
56 <option value="all">All ORFs/CDSs from each sequence</option> | |
57 <option value="top">All ORFs/CDSs from each sequence with the maximum length</option> | |
58 <option value="one">First ORF/CDS from each sequence with the maximum length</option> | |
59 </param> | |
60 <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)" /> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
61 <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 | 62 <option value="both">Search both the forward and reverse strand</option> |
63 <option value="forward">Only search the forward strand</option> | |
64 <option value="reverse">Only search the reverse strand</option> | |
65 </param> | |
66 </inputs> | |
67 <outputs> | |
68 <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" /> | |
69 <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" /> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
70 <data name="out_bed_file" format="bed6" label="${ftype.value}s (bed)" /> |
8 | 71 <data name="out_gff3_file" format="gff3" label="${ftype.value}s (gff3)" /> |
5 | 72 </outputs> |
73 <tests> | |
74 <test> | |
75 <param name="input_file" value="get_orf_input.fasta" /> | |
76 <param name="table" value="1" /> | |
77 <param name="ftype" value="CDS" /> | |
78 <param name="ends" value="open" /> | |
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.t1_nuc_out.fasta" /> | |
83 <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" /> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
84 <output name="out_bed_file" file="get_orf_input.t1_bed_out.bed" /> |
8 | 85 <output name="out_gff3_file" file="get_orf_input.t1_gff3_out.gff3" /> |
5 | 86 </test> |
87 <test> | |
88 <param name="input_file" value="get_orf_input.fasta" /> | |
89 <param name="table" value="11" /> | |
90 <param name="ftype" value="CDS" /> | |
91 <param name="ends" value="closed" /> | |
92 <param name="mode" value="all" /> | |
93 <param name="min_len" value="10" /> | |
94 <param name="strand" value="forward" /> | |
95 <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" /> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
96 <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" /> |
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
97 <output name="out_bed_file" file="get_orf_input.t11_bed_out.bed" /> |
8 | 98 <output name="out_gff3_file" file="get_orf_input.t11_gff3_out.gff3" /> |
5 | 99 </test> |
100 <test> | |
101 <param name="input_file" value="get_orf_input.fasta" /> | |
102 <param name="table" value="11" /> | |
103 <param name="ftype" value="CDS" /> | |
104 <param name="ends" value="open" /> | |
105 <param name="mode" value="all" /> | |
106 <param name="min_len" value="10" /> | |
107 <param name="strand" value="forward" /> | |
108 <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" /> | |
109 <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" /> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
110 <output name="out_bed_file" file="get_orf_input.t11_open_bed_out.bed" /> |
8 | 111 <output name="out_gff3_file" file="get_orf_input.t11_open_gff3_out.gff3" /> |
5 | 112 </test> |
113 <test> | |
114 <param name="input_file" value="Ssuis.fasta" /> | |
115 <param name="table" value="11" /> | |
116 <param name="ftype" value="ORF" /> | |
117 <param name="ends" value="open" /> | |
118 <param name="mode" value="all" /> | |
119 <param name="min_len" value="100" /> | |
120 <param name="strand" value="both" /> | |
121 <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" /> | |
122 <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" /> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
123 <output name="out_bed_file" file="get_orf_input.Suis_ORF.bed" /> |
8 | 124 <output name="out_gff3_file" file="get_orf_input.Suis_ORF.gff3" /> |
5 | 125 </test> |
126 </tests> | |
127 <help> | |
128 **What it does** | |
129 | |
130 Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ | |
131 and Standard Flowgram Format (SFF) are supported), and searches each sequence | |
132 for open reading frames (ORFs) or potential coding sequences (CDSs) of the | |
133 given minimum length. These are returned as FASTA files of nucleotides and | |
134 protein sequences. | |
135 | |
136 You can choose to have all the ORFs/CDSs above the minimum length for each | |
137 sequence (similar to the EMBOSS getorf tool), those with the longest length | |
138 equal, or the first ORF/CDS with the longest length (in the special case | |
139 where a sequence encodes two or more long ORFs/CDSs of the same length). The | |
140 last option is a reasonable choice when the input sequences represent EST or | |
141 mRNA sequences, where only one ORF/CDS is expected. | |
142 | |
143 Note that if no ORFs/CDSs in a sequence match the criteria, there will be no | |
144 output for that sequence. | |
145 | |
146 Also note that the ORFs/CDSs are assigned modified identifiers to distinguish | |
147 them from the original full length sequences, by appending a suffix. | |
148 | |
149 The start and stop codons are taken from the `NCBI Genetic Codes | |
150 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_. | |
151 When searching for ORFs, the sequences will run from stop codon to stop | |
152 codon, and any start codons are ignored. When searching for CDSs, the first | |
153 potential start codon will be used, giving the longest possible CDS within | |
154 each ORF, and thus the longest possible protein sequence. This is useful | |
155 for things like BLAST or domain searching, but since this may not be the | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
156 correct start codon, it may not be appropriate for signal peptide detection |
5 | 157 etc. |
158 | |
159 **Example Usage** | |
160 | |
161 Given some EST sequences (Sanger capillary reads) assembled into unigenes, | |
162 or a transcriptome assembly from some RNA-Seq, each of your nucleotide | |
163 sequences should (barring sequencing, assembly errors, frame-shifts etc) | |
164 encode one protein as a single ORF/CDS, which you wish to extract (and | |
165 perhaps translate into amino acids). | |
166 | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
167 If your RNA-Seq data was strand specific, and assembled taking this into |
5 | 168 account, you should only search for ORFs/CDSs on the forward strand. |
169 | |
170 **Citation** | |
171 | |
172 If you use this Galaxy tool in work leading to a scientific publication please | |
173 cite the following paper: | |
174 | |
175 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
176 Galaxy tools and workflows for sequence analysis with applications | |
177 in molecular plant pathology. PeerJ 1:e167 | |
178 http://dx.doi.org/10.7717/peerj.167 | |
179 | |
180 This tool uses Biopython, so you may also wish to cite the Biopython | |
181 application note (and Galaxy too of course): | |
182 | |
183 Cock et al (2009). Biopython: freely available Python tools for computational | |
184 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
185 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
186 | |
187 This tool is available to install into other Galaxy Instances via the Galaxy | |
188 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss | |
189 </help> | |
7
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
190 <citations> |
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
191 <citation type="doi">10.7717/peerj.167</citation> |
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
192 <citation type="doi">10.1093/bioinformatics/btp163</citation> |
705a2e2df7fb
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
peterjc
parents:
5
diff
changeset
|
193 </citations> |
5 | 194 </tool> |