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author cpt
date Fri, 05 Jan 2024 05:52:07 +0000
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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">
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2 <description>e.g. to get peptides from ESTs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.9.16">python</requirement>
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9 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
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10 <requirement type="package" version="1.81">biopython</requirement>
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11 <requirement type="package" version="2022.1.18">regex</requirement>
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12 </expand>
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13 <command interpreter="python" detect_errors="aggressive"><![CDATA[
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14 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' ]]>
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15 </command>
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16 <inputs>
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17 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format."/>
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18 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
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19 <option value="1">1. Standard</option>
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20 <option value="2">2. Vertebrate Mitochondrial</option>
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21 <option value="3">3. Yeast Mitochondrial</option>
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22 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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23 <option value="5">5. Invertebrate Mitochondrial</option>
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24 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option>
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25 <option value="9">9. Echinoderm Mitochondrial</option>
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26 <option value="10">10. Euplotid Nuclear</option>
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27 <option value="11">11. Bacterial</option>
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28 <option value="12">12. Alternative Yeast Nuclear</option>
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29 <option value="13">13. Ascidian Mitochondrial</option>
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30 <option value="14">14. Flatworm Mitochondrial</option>
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31 <option value="15">15. Blepharisma Macronuclear</option>
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32 <option value="16">16. Chlorophycean Mitochondrial</option>
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33 <option value="21">21. Trematode Mitochondrial</option>
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34 <option value="22">22. Scenedesmus obliquus</option>
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35 <option value="23">23. Thraustochytrium Mitochondrial</option>
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36 <option value="24">24. Pterobranchia Mitochondrial</option>
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37 </param>
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38 <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs">
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39 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option>
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40 <option value="CDS">Look for CDSs (with start and stop codons)</option>
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41 </param>
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42 <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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43 <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).">
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44 <option value="both">Search both the forward and reverse strand</option>
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45 <option value="forward">Only search the forward strand</option>
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46 <option value="reverse">Only search the reverse strand</option>
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47 </param>
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48 </inputs>
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49 <outputs>
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50 <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)"/>
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51 <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)"/>
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52 <data name="out_bed_file" format="bed6" label="${ftype.value}s (bed)"/>
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53 <data name="out_gff3_file" format="gff3" label="${ftype.value}s (gff3)"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input_file" value="Orf_T7In.fasta"/>
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58 <param name="table" value="11"/>
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59 <param name="ftype" value="ORF"/>
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60 <param name="min_len" value="30"/>
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61 <param name="strand" value="both"/>
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62 <output name="out_nuc_file" file="Orf_T7Out_Nuc.fasta"/>
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63 <output name="out_prot_file" file="Orf_T7Out_AA.fasta"/>
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64 <output name="out_bed_file" file="Orf_T7Out_Bed.bed"/>
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65 <output name="out_gff3_file" file="Orf_T7Out_Gff.gff3"/>
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66 </test>
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67 <test>
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68 <param name="input_file" value="Orf_In2.fasta"/>
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69 <param name="table" value="1"/>
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70 <param name="ftype" value="CDS"/>
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71 <param name="min_len" value="10"/>
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72 <param name="strand" value="forward"/>
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73 <output name="out_nuc_file" file="Orf_Out2T1_Nuc.fasta"/>
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74 <output name="out_prot_file" file="Orf_Out2T1_AA.fasta"/>
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75 <output name="out_bed_file" file="Orf_Out2T1_Bed.bed"/>
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76 <output name="out_gff3_file" file="Orf_Out2T1_Gff.gff3"/>
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77 </test>
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78 <test>
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79 <param name="input_file" value="Orf_In2.fasta"/>
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80 <param name="table" value="11"/>
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81 <param name="ftype" value="CDS"/>
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82 <param name="min_len" value="10"/>
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83 <param name="strand" value="forward"/>
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84 <output name="out_nuc_file" file="Orf_Out2T11_Nuc.fasta"/>
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85 <output name="out_prot_file" file="Orf_Out2T11_AA.fasta"/>
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86 <output name="out_bed_file" file="Orf_Out2T11_Bed.bed"/>
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87 <output name="out_gff3_file" file="Orf_Out2T11_Gff.gff3"/>
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88 </test>
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89 </tests>
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90 <help>
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91 **What it does**
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92
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93 Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ
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94 and Standard Flowgram Format (SFF) are supported), and searches each sequence
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95 for open reading frames (ORFs) or potential coding sequences (CDSs) of the
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96 given minimum length. These are returned as FASTA files of nucleotides and
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97 protein sequences.
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98
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99 You can choose to have all the ORFs/CDSs above the minimum length for each
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100 sequence (similar to the EMBOSS getorf tool), those with the longest length
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101 equal, or the first ORF/CDS with the longest length (in the special case
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102 where a sequence encodes two or more long ORFs/CDSs of the same length). The
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103 last option is a reasonable choice when the input sequences represent EST or
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104 mRNA sequences, where only one ORF/CDS is expected.
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105
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106 Note that if no ORFs/CDSs in a sequence match the criteria, there will be no
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107 output for that sequence.
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108
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109 Also note that the ORFs/CDSs are assigned modified identifiers to distinguish
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110 them from the original full length sequences, by appending a suffix.
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111
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112 The start and stop codons are taken from the `NCBI Genetic Codes
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113 &lt;http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi&gt;`_.
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114 When searching for ORFs, the sequences will run from stop codon to stop
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115 codon, and any start codons are ignored. When searching for CDSs, the first
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116 potential start codon will be used, giving the longest possible CDS within
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117 each ORF, and thus the longest possible protein sequence. This is useful
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118 for things like BLAST or domain searching, but since this may not be the
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119 correct start codon, it may not be appropriate for signal peptide detection
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120 etc.
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121
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122 **Example Usage**
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123
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124 Given some EST sequences (Sanger capillary reads) assembled into unigenes,
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125 or a transcriptome assembly from some RNA-Seq, each of your nucleotide
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126 sequences should (barring sequencing, assembly errors, frame-shifts etc)
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127 encode one protein as a single ORF/CDS, which you wish to extract (and
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128 perhaps translate into amino acids).
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129
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130 If your RNA-Seq data was strand specific, and assembled taking this into
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131 account, you should only search for ORFs/CDSs on the forward strand.
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132
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133 **Citation**
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134
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135 If you use this Galaxy tool in work leading to a scientific publication please
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136 cite the following paper:
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137
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138 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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139 Galaxy tools and workflows for sequence analysis with applications
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140 in molecular plant pathology. PeerJ 1:e167
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141 http://dx.doi.org/10.7717/peerj.167
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142
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143 This tool uses Biopython, so you may also wish to cite the Biopython
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144 application note (and Galaxy too of course):
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145
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146 Cock et al (2009). Biopython: freely available Python tools for computational
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147 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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148 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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149
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150 This tool is available to install into other Galaxy Instances via the Galaxy
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151 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
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152 </help>
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153 <citations>
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154 <citation type="doi">10.7717/peerj.167</citation>
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155 <citation type="doi">10.1093/bioinformatics/btp163</citation>
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156 </citations>
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157 </tool>