[2] | 1 | <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
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| 2 | <description>Align nucleic coding regions given the aligned proteins</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $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>Nucleic Sequences</label>
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| 8 | </param>
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| 9 | <param format="data" name="input2" type="data">
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| 10 | <label>Protein Sequences</label>
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| 11 | </param>
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| 12 | <param name="table" type="select">
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| 13 | <label>Code to use</label>
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| 14 | <option value="0">Standard</option>
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| 15 | <option value="1">Standard (with alternative initiation codons)</option>
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| 16 | <option value="2">Vertebrate Mitochondrial</option>
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| 17 | <option value="3">Yeast Mitochondrial</option>
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| 18 | <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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| 19 | <option value="5">Invertebrate Mitochondrial</option>
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| 20 | <option value="6">Ciliate Macronuclear and Dasycladacean</option>
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| 21 | <option value="9">Echinoderm Mitochondrial</option>
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| 22 | <option value="10">Euplotid Nuclear</option>
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| 23 | <option value="11">Bacterial</option>
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| 24 | <option value="12">Alternative Yeast Nuclear</option>
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| 25 | <option value="13">Ascidian Mitochondrial</option>
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| 26 | <option value="14">Flatworm Mitochondrial</option>
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| 27 | <option value="15">Blepharisma Macronuclear</option>
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| 28 | <option value="16">Chlorophycean Mitochondrial</option>
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| 29 | <option value="21">Trematode Mitochondrial</option>
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| 30 | <option value="22">Scenedesmus obliquus</option>
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| 31 | <option value="23">Thraustochytrium Mitochondrial</option>
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| 32 | </param>
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| 33 | <param name="out_format1" type="select">
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| 34 | <label>Output Sequence File Format</label>
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| 35 | <option value="fasta">FASTA (m)</option>
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| 36 | <option value="acedb">ACeDB (m)</option>
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| 37 | <option value="asn1">ASN.1 (m)</option>
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| 38 | <option value="clustal">Clustal (m)</option>
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| 39 | <option value="codata">CODATA (m)</option>
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| 40 | <option value="embl">EMBL (m)</option>
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| 41 | <option value="fitch">Fitch (m)</option>
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| 42 | <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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| 43 | <option value="genbank">GENBANK (m)</option>
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| 44 | <option value="gff">GFF (m)</option>
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| 45 | <option value="hennig86">Hennig86 (m)</option>
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| 46 | <option value="ig">Intelligenetics (m)</option>
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| 47 | <option value="jackknifer">Jackknifer (m)</option>
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| 48 | <option value="jackknifernon">Jackknifernon (m)</option>
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| 49 | <option value="mega">Mega (m)</option>
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| 50 | <option value="meganon">Meganon (m)</option>
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| 51 | <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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| 52 | <option value="pir">NBRF (PIR) (m)</option>
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| 53 | <option value="ncbi">NCBI style FASTA (m)</option>
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| 54 | <option value="nexus">Nexus/PAUP (m)</option>
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| 55 | <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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| 56 | <option value="phylip">PHYLIP interleaved (m)</option>
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| 57 | <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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| 58 | <option value="selex">SELEX (m)</option>
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| 59 | <option value="staden">Staden (s)</option>
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| 60 | <option value="strider">DNA strider (m)</option>
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| 61 | <option value="swiss">SwisProt entry (m)</option>
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| 62 | <option value="text">Plain sequence (s)</option>
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| 63 | <option value="treecon">Treecon (m)</option>
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| 64 | </param>
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| 65 | </inputs>
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| 66 | <outputs>
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| 67 | <data format="fasta" name="out_file1" />
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| 68 | </outputs> |
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| 69 | <tests> |
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| 70 | <test> |
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| 71 | <param name="input1" value="3.fasta"/> |
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| 72 | <param name="input2" value="2.pep"/> |
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| 73 | <param name="table" value="0"/> |
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| 74 | <param name="out_format1" value="fasta"/> |
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| 75 | <output name="out_file1" file="emboss_tranalign_out.fasta"/> |
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| 76 | </test> |
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| 77 | </tests>
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| 78 | <code file="emboss_format_corrector.py" />
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| 79 | <help> |
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| 80 | You can view the original documentation here_. |
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| 81 | |
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| 82 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html |
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| 83 | </help> |
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| 84 | </tool> |
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