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annotate emboss_tranalign.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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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
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84 ------
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85
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86 **Citation**
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88 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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90 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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91 </help>
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92 </tool>