[2] | 1 | <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
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| 2 | <description>Translate nucleic acid sequences</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
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| 5 | <inputs>
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| 6 | <param format="fasta" name="input1" type="data">
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| 7 | <label>Sequences</label>
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| 8 | </param>
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| 9 | <param name="frame" type="select">
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| 10 | <label>Frame(s) to translate</label>
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| 11 | <option value="1">Frame 1</option>
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| 12 | <option value="2">Frame 2</option>
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| 13 | <option value="3">Frame 3</option>
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| 14 | <option value="F">Forward three frames</option>
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| 15 | <option value="-1">Frame -1</option>
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| 16 | <option value="-2">Frame -2</option>
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| 17 | <option value="-3">Frame -3</option>
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| 18 | <option value="R">Reverse three frames</option>
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| 19 | <option value="6">All six frames</option>
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| 20 | </param>
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| 21 | <param name="table" type="select">
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| 22 | <label>Code to use</label>
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| 23 | <option value="0">Standard</option>
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| 24 | <option value="1">Standard (with alternative initiation codons)</option>
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| 25 | <option value="2">Vertebrate Mitochondrial</option>
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| 26 | <option value="3">Yeast Mitochondrial</option>
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| 27 | <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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| 28 | <option value="5">Invertebrate Mitochondrial</option>
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| 29 | <option value="6">Ciliate Macronuclear and Dasycladacean</option>
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| 30 | <option value="9">Echinoderm Mitochondrial</option>
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| 31 | <option value="10">Euplotid Nuclear</option>
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| 32 | <option value="11">Bacterial</option>
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| 33 | <option value="12">Alternative Yeast Nuclear</option>
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| 34 | <option value="13">Ascidian Mitochondrial</option>
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| 35 | <option value="14">Flatworm Mitochondrial</option>
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| 36 | <option value="15">Blepharisma Macronuclear</option>
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| 37 | <option value="16">Chlorophycean Mitochondrial</option>
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| 38 | <option value="21">Trematode Mitochondrial</option>
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| 39 | <option value="22">Scenedesmus obliquus</option>
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| 40 | <option value="23">Thraustochytrium Mitochondrial</option>
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| 41 | </param>
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| 42 | <param name="regions" size="10" type="text" value="">
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| 43 | <label>Regions to translate</label>
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| 44 | </param>
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| 45 | <param name="trim" type="select">
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| 46 | <label>Remove all 'X' and '*' characters from the right end of the translation</label>
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| 47 | <option value="no">No</option>
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| 48 | <option value="yes">Yes</option>
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| 49 | </param>
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| 50 | <param name="clean" type="select">
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| 51 | <label>Change all STOP codon positions from the '*' character to 'X'</label>
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| 52 | <option value="no">No</option>
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| 53 | <option value="yes">Yes</option>
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| 54 | </param>
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| 55 | <param name="alternative" type="select">
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| 56 | <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label>
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| 57 | <option value="no">No</option>
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| 58 | <option value="yes">Yes</option>
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| 59 | </param>
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| 60 | <param name="out_format1" type="select">
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| 61 | <label>Output Sequence File Format</label>
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| 62 | <option value="fasta">FASTA (m)</option>
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| 63 | <option value="acedb">ACeDB (m)</option>
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| 64 | <option value="asn1">ASN.1 (m)</option>
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| 65 | <option value="clustal">Clustal (m)</option>
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| 66 | <option value="codata">CODATA (m)</option>
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| 67 | <option value="embl">EMBL (m)</option>
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| 68 | <option value="fitch">Fitch (m)</option>
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| 69 | <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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| 70 | <option value="genbank">GENBANK (m)</option>
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| 71 | <option value="gff">GFF (m)</option>
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| 72 | <option value="hennig86">Hennig86 (m)</option>
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| 73 | <option value="ig">Intelligenetics (m)</option>
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| 74 | <option value="jackknifer">Jackknifer (m)</option>
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| 75 | <option value="jackknifernon">Jackknifernon (m)</option>
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| 76 | <option value="mega">Mega (m)</option>
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| 77 | <option value="meganon">Meganon (m)</option>
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| 78 | <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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| 79 | <option value="pir">NBRF (PIR) (m)</option>
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| 80 | <option value="ncbi">NCBI style FASTA (m)</option>
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| 81 | <option value="nexus">Nexus/PAUP (m)</option>
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| 82 | <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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| 83 | <option value="phylip">PHYLIP interleaved (m)</option>
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| 84 | <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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| 85 | <option value="selex">SELEX (m)</option>
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| 86 | <option value="staden">Staden (s)</option>
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| 87 | <option value="strider">DNA strider (m)</option>
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| 88 | <option value="swiss">SwisProt entry (m)</option>
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| 89 | <option value="text">Plain sequence (s)</option>
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| 90 | <option value="treecon">Treecon (m)</option>
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| 91 | </param>
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| 92 | </inputs>
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| 93 | <outputs>
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| 94 | <data format="fasta" name="out_file1" />
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| 95 | </outputs> |
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| 96 | <tests> |
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| 97 | <test> |
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| 98 | <param name="input1" value="2.fasta"/> |
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| 99 | <param name="frame" value="1"/> |
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| 100 | <param name="table" value="0"/> |
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| 101 | <param name="regions" value=""/> |
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| 102 | <param name="trim" value="no"/> |
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| 103 | <param name="clean" value="no"/> |
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| 104 | <param name="alternative" value="no"/> |
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| 105 | <param name="out_format1" value="fasta"/> |
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| 106 | <output name="out_file1" file="emboss_transeq_out.fasta"/> |
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| 107 | </test> |
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| 108 | </tests>
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| 109 | <code file="emboss_format_corrector.py" />
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| 110 | <help> |
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| 111 | |
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| 112 | .. class:: warningmark |
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| 113 | |
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| 114 | The input dataset needs to be sequences. |
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| 115 | |
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| 116 | ----- |
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| 117 | |
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| 118 | You can view the original documentation here_. |
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| 119 | |
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| 120 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html |
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| 121 | </help> |
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| 122 | </tool> |
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