Mercurial > repos > devteam > emboss_5

annotate emboss_transeq.xml @ 18:c2228166c035 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"
author iuc
date Fri, 20 Nov 2020 16:49:40 +0000
parents 27c43fb015f0
children 21a9fb508031
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14
27c43fb015f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
iuc
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1 <tool id="EMBOSS: transeq101" name="transeq" version="@VERSION@">
13
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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2 <description>Translate nucleic acid sequences</description>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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3 <macros>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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4 <import>macros.xml</import>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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5 </macros>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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6 <expand macro="requirements" />
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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7 <code file="emboss_format_corrector.py" />
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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8 <command detect_errors="aggressive"><![CDATA[
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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9 transeq
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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10 -sequence '$input1'
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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11 -outseq '$out_file1'
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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12 -frame $frame
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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13 -table $table
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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14 #if str($regions).strip():
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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15 -regions '$regions'
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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16 #end if
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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17 -trim $trim
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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18 -clean $clean
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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19 -alternative $alternative
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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20 -osformat2 '$out_format1'
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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21 -auto
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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22 ]]></command>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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23 <inputs>
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24 <param name="input1" argument="-sequence" type="data" format="fasta" label="Sequences" />
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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25 <param argument="-frame" type="select" label="Frame(s) to translate">
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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26 <option value="1">Frame 1</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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27 <option value="2">Frame 2</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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28 <option value="3">Frame 3</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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29 <option value="F">Forward three frames</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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30 <option value="-1">Frame -1</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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31 <option value="-2">Frame -2</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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32 <option value="-3">Frame -3</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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33 <option value="R">Reverse three frames</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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34 <option value="6">All six frames</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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35 </param>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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36 <param argument="-table" type="select" label="Code to use">
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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37 <option value="0">Standard</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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38 <option value="1">Standard (with alternative initiation codons)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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39 <option value="2">Vertebrate Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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40 <option value="3">Yeast Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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41 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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42 <option value="5">Invertebrate Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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43 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
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iuc
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44 <option value="9">Echinoderm Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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45 <option value="10">Euplotid Nuclear</option>
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iuc
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46 <option value="11">Bacterial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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47 <option value="12">Alternative Yeast Nuclear</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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48 <option value="13">Ascidian Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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49 <option value="14">Flatworm Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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50 <option value="15">Blepharisma Macronuclear</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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51 <option value="16">Chlorophycean Mitochondrial</option>
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52 <option value="21">Trematode Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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53 <option value="22">Scenedesmus obliquus</option>
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54 <option value="23">Thraustochytrium Mitochondrial</option>
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55 </param>
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56 <param argument="-regions" type="text" value="" label="Regions to translate" />
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iuc
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57 <param argument="-trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation">
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58 <option value="no">No</option>
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59 <option value="yes">Yes</option>
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60 </param>
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61 <param argument="-clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'">
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62 <option value="no">No</option>
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63 <option value="yes">Yes</option>
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64 </param>
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65 <param argument="-alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence">
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66 <option value="no">No</option>
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67 <option value="yes">Yes</option>
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68 </param>
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69 <param name="out_format1" argument="-osformat2" type="select" label="Output sequence file format">
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70 <option value="fasta">FASTA (m)</option>
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71 <option value="acedb">ACeDB (m)</option>
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72 <option value="asn1">ASN.1 (m)</option>
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73 <option value="clustal">Clustal (m)</option>
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74 <option value="codata">CODATA (m)</option>
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75 <option value="embl">EMBL (m)</option>
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76 <option value="fitch">Fitch (m)</option>
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77 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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78 <option value="genbank">GENBANK (m)</option>
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79 <option value="gff">GFF (m)</option>
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80 <option value="hennig86">Hennig86 (m)</option>
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81 <option value="ig">Intelligenetics (m)</option>
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82 <option value="jackknifer">Jackknifer (m)</option>
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83 <option value="jackknifernon">Jackknifernon (m)</option>
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84 <option value="mega">Mega (m)</option>
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85 <option value="meganon">Meganon (m)</option>
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86 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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87 <option value="pir">NBRF (PIR) (m)</option>
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88 <option value="ncbi">NCBI style FASTA (m)</option>
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89 <option value="nexus">Nexus/PAUP (m)</option>
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90 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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91 <option value="phylip">PHYLIP interleaved (m)</option>
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92 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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93 <option value="selex">SELEX (m)</option>
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94 <option value="staden">Staden (s)</option>
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95 <option value="strider">DNA strider (m)</option>
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96 <option value="swiss">SwisProt entry (m)</option>
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97 <option value="text">Plain sequence (s)</option>
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98 <option value="treecon">Treecon (m)</option>
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99 </param>
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100 </inputs>
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101 <outputs>
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102 <data name="out_file1" format="fasta" />
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103 </outputs>
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104 <tests>
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105 <test>
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106 <param name="input1" value="2.fasta"/>
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107 <param name="frame" value="1"/>
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108 <param name="table" value="0"/>
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109 <param name="regions" value=""/>
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110 <param name="trim" value="no"/>
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111 <param name="clean" value="no"/>
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112 <param name="alternative" value="no"/>
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113 <param name="out_format1" value="fasta"/>
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114 <output name="out_file1" file="emboss_transeq_out.fasta"/>
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115 </test>
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116 </tests>
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117 <help><![CDATA[
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118 .. class:: warningmark
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119
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120 The input dataset needs to be sequences.
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121
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122 -----
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123
13
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124 You can view the original documentation here_.
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125
13
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126 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html
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127 ]]></help>
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128 <expand macro="citations" />
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129 </tool>