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1 <tool id="igblastn" name="igBLASTn" version="0.1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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4 igblast/igblast.sh $input $species $locus $output
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="fasta" label="Fasta file"/>
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8 <param name="species" type="select" label="Species">
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9 <option value="human">Homo sapiens</option>
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10 <option value="mouse">Mus musculus</option>
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11 <option value="rat">Rattus norvegicus</option>
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12 <option value="rabbit">Oryctolagus cuniculus</option>
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13 <option value="rhesus_monkey">Macaca mulatta</option>
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14 <option value="BosTaurus">BosTaurus</option>
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15 <option value="CamelusDromedarius">CamelusDromedarius</option>
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16 <option value="CanisLupusFamiliaris">CanisLupusFamiliaris</option>
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17 <option value="DanioRerio">DanioRerio</option>
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18 <option value="MusSpretus">MusSpretus</option>
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19 <option value="OncorhynchusMykiss">OncorhynchusMykiss</option>
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20 <option value="SusScrofa">SusScrofa</option>
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21 <option value="GallusGallus">GallusGallus</option>
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22 <option value="AnasPlatyrhynchos">AnasPlatyrhynchos</option>
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23 </param>
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24 <param name="locus" type="select" label="Locus">
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25 <option value="TRA">TRA</option>
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26 <option value="TRB">TRB</option>
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27 <option value="TRG">TRG</option>
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28 <option value="TRD">TRD</option>
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29 <option value="IGH">IGH</option>
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30 <option value="IGK">IGK</option>
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31 <option value="IGL">IGL</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="output" format="tabular" type="data" label="${input.name}-igBLASTn aligned"/>
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36 <!--<data name="log" format="text" label="log"/>-->
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37 </outputs>
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38 <requirements>
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39 <requirement type="package" version="0.6">igblastwrp</requirement>
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40 </requirements>
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41 <help>
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42 ============
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43 iReport
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44 ============
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45
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46 This tool uses the online igBLAST website hosted by NCBI to blast a FASTA file, it retrieves the result and generates a convenient tabular format for further processing.
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47
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48 **NOTE**
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49
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50 .. class:: warningmark
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51
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52 - Everything goes through the servers of NCBI, so if you have sensitive data that that isn't allowed to leave your local network, this isn't the tool the use.
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53
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54 **USAGE**
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55
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56 .. class:: infomark
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57
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58 - This tool uses a free service provided by NCBI, and although there doesn't seem to be any restrictions on usage, avoid unnecessary usage to lighten the load on NCBI's servers.
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59
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60
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61 **INPUT**
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62
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63 This tool accepts FASTA files as input:
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64
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65 ::
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66
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67 >lcl|FLN1FA002RWEZA.1|
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68 ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatc
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69 tccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgc
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70 gagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcct
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71 cag
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72 >lcl|FLN1FA001BLION.1|
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73 aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccat
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74 taccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtg
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75 cgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag
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76
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77 **OUTPUT**
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78
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79 The following data is used for ARGalaxy
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80
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81 +-----------------+----------------------------------------------+
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82 | Column name | Column contents |
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83 +-----------------+----------------------------------------------+
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84 | ID | The Sequence ID provided by the sequencer. |
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85 +-----------------+----------------------------------------------+
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86 | VDJ Frame | In-frame/Out-frame |
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87 +-----------------+----------------------------------------------+
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88 | Top V Gene | The best matching V gene found. |
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89 +-----------------+----------------------------------------------+
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90 | Top D Gene | The best matching D gene found. |
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91 +-----------------+----------------------------------------------+
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92 | Top J Gene | The best matching J gene found. |
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93 +-----------------+----------------------------------------------+
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94 | CDR3 Seq | The CDR3 region. |
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95 +-----------------+----------------------------------------------+
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96 | CDR3 Length | The length of the CDR3 region. |
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97 +-----------------+----------------------------------------------+
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98 | CDR3 Seq DNA | The CDR3 sequence region. |
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99 +-----------------+----------------------------------------------+
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100 | CDR3 Length DNA | The length of the CDR3 sequence region. |
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101 +-----------------+----------------------------------------------+
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102 | Functionality | If sequence is productive/unproductive |
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103 +-----------------+----------------------------------------------+
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104
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105
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106 </help>
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107 </tool>
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